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Marčiulynas A, Menkis A. Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur. MICROBIAL ECOLOGY 2024; 87:27. [PMID: 38175304 DOI: 10.1007/s00248-023-02334-3] [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: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.
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Affiliation(s)
- Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101, Kaunas District, Lithuania.
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
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2
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Pioli S, Clagnan E, Chowdhury AA, Bani A, Borruso L, Ventura M, Tonon G, Brusetti L. Structural and functional microbial diversity in deadwood respond to decomposition dynamics. Environ Microbiol 2023; 25:2351-2367. [PMID: 37403552 DOI: 10.1111/1462-2920.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.
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Affiliation(s)
- Silvia Pioli
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo (RM), Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Atif Aziz Chowdhury
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Alessia Bani
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Maurizio Ventura
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Giustino Tonon
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
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3
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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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Ramberg E, Berglund H, Penttilä R, Strengbom J, Jönsson M. Prescribed fire is an effective restoration measure for increasing boreal fungal diversity. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2892. [PMID: 37232443 DOI: 10.1002/eap.2892] [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: 01/12/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Intensive forestry practices have had a negative impact on boreal forest biodiversity; as a consequence, the need for restoration is pressing. Polypores (wood-inhabiting fungi) are key decomposers of dead wood, but, due to a lack of coarse woody debris (CWD) in forest ecosystems, many species are under threat. Here, we study the long-term effects on polypore diversity of two restoration treatments: creating CWD by felling whole trees and prescribed burning. This large-scale experiment is located in spruce-dominated boreal forests in southern Finland. The experiment has a factorial design (n = 3) including three levels of created CWD (5, 30, and 60 m3 ha-1 ) crossed with burning or no burning. In 2018, 16 years after launching the experiment, we inventoried polypores on 10 experimentally cut logs and 10 naturally fallen logs per stand. We found that overall polypore community composition differed between burned and unburned stands. However, only red-listed species abundances and richness were positively affected by prescribed burning. We found no effects of CWD levels created mechanically by felling of trees. We show, for the first time, that prescribed burning is an effective measure for restoring polypore diversity in a late-successional Norway spruce forest. Burning creates CWD with certain characteristics that differ from what is created by CWD restoration by felling trees. Prescribed burning promotes primarily red-listed species, demonstrating its effectiveness as a restoration measure to promote diversity of threatened polypore species in boreal forests. However, because the CWD that the burning creates will decrease over time, to be functional, prescribed burns need to be applied regularly on the landscape scale. Large-scale and long-term experimental studies, such as this one, are invaluable for establishing evidence-based restoration strategies.
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Affiliation(s)
- Ellinor Ramberg
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Håkan Berglund
- Swedish Species Information Centre, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Reijo Penttilä
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Joachim Strengbom
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Mari Jönsson
- Swedish Species Information Centre, Swedish University of Agricultural Science, Uppsala, Sweden
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5
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Substrate affinities of wood decay fungi are foremost structured by wood properties not climate. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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6
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Mali T, Laine K, Hamberg L, Lundell T. Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Besserer A, Rose C, Deveau A. Visualization of Fungi During Wood Colonization and Decomposition by Microscopy: From Light to Electron Microscopy. Methods Mol Biol 2022; 2605:337-361. [PMID: 36520402 DOI: 10.1007/978-1-0716-2871-3_17] [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] [Indexed: 12/16/2022]
Abstract
Fungi are the principal decomposers of wood together with xylophage insects and, as such, have a central role in nutrient cycling of forest ecosystems. These fungi are also envisaged as promising tools for converting wood and waste of wood industries into chemicals, as alternative to fossil chemicals. At the same time, wood decomposers pose a threat to wooden building materials and are intensively fought. As a consequence, intense researches have been conducted over the past 50 years to identify the fungi responsible for wood decomposition, the mechanisms by which they do so, the wood properties involved in resistance or sensitivity to attacks and ways to preserve woods. Many tools are now available to study fungal colonization of wood, including: "omics" techniques, enzymatic assays, spectrometry, etc. However, all these approaches provide bulk information and the data obtained by these methods contain no information on the localization of fungi, the stage of decomposition of the wood and the potential interactions between microorganisms. In these regards, microscopy approaches provide complementary information that can strengthen conclusions. The present chapter describes a diverse range of microscopy approaches, from simple bench light microscopy to confocal and electron microscopies, to shed light on the way fungi colonize wood tissues.
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Affiliation(s)
| | - Christophe Rose
- Université de Lorraine, INRAE, UMR SILVA, Champenoux, France
| | - Aurélie Deveau
- University de Lorraine, INRAE, UMR1136 Interactions arbre microorganismes, Centre INRAE Grand Est -Nancy, Champenoux, France.
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Microbial Community Succession Associated with Poplar Wood Discoloration. PLANTS 2022; 11:plants11182420. [PMID: 36145822 PMCID: PMC9504049 DOI: 10.3390/plants11182420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022]
Abstract
Microbes are common inhabitants of wood, but little is known about the relationship between microbial community dynamics during wood discoloration. This study uses simulation experiments to examine the changes in the microbial communities in poplar wood at different succession stages. The composition and structure of the microbial communities changed significantly in different successional stages, with an overarching pattern of bacterial diversity decreasing and fungal diversity increasing from the early to the late successional stages. Nevertheless, succession did not affect the composition of the microbial communities at the phylum level: Proteobacteria and Acidobacteria dominated the bacterial communities, while Ascomycota and Basidiomycota dominated the fungal communities. However, at the genus level, bacterial populations of Sphingomonas and Methylobacterium, and fungal populations of Sphaeropsis were significantly more prevalent in later successional stages. Stochastic assembly processes were dominant in the early successional stages for bacteria and fungi. However, variable selection played a more critical role in the assembly processes as succession proceeded, with bacterial communities evolving towards more deterministic processes and fungal communities towards more stochastic processes. Altogether, our results suggest that bacteria and fungi exhibit different ecological strategies in poplar wood. Understanding those strategies, the resulting changes in community structures over time, and the relationship to the different stages of poplar discoloration, is vital to the biological control of that discoloration.
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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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10
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Prylutskyi O, Yatsiuk I, Savchenko A, Kit M, Solodiankin O, Schigel D. Strict substrate requirements alongside rapid substrate turnover may indicate an early colonization: A case study of Pleurotus calyptratus (Agaricales, Basidiomycota). FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cuff JP, Windsor FM, Gilmartin EC, Boddy L, Jones TH. Influence of European Beech (Fagales: Fagaceae) Rot Hole Habitat Characteristics on Invertebrate Community Structure and Diversity. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6374214. [PMID: 34553221 PMCID: PMC8458099 DOI: 10.1093/jisesa/ieab071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 06/13/2023]
Abstract
Hollows of veteran trees (i.e., rot holes) provide habitat for many rare and threatened saproxylic invertebrates. Rot holes are highly heterogeneous, particularly in terms of substrate and microclimate conditions. There is, however, a dearth of information regarding the differences in biological communities inhabiting rot holes with different environmental conditions. Invertebrates were sampled from European beech (Fagus sylvatica) rot holes in Windsor, Savernake, and Epping Forests (United Kingdom). For each rot hole, physical and environmental conditions were measured, including tree diameter, rot hole dimensions, rot hole height, substrate density, water content, and water potential. These parameters were used to assess the influence of environmental conditions and habitat characteristics on invertebrate communities. Rot hole invertebrate communities were extremely diverse, containing both woodland generalist and saproxylic specialist taxa. Large variation in community structure was observed between rot holes and across woodlands; all sites supported threatened and endangered taxa. Environmental conditions in rot holes were highly variable within and between woodland sites, and communities were predominantly structured by these environmental conditions. In particular, turnover between invertebrate communities was linked to high β-diversity. The linked heterogeneity of environmental conditions and invertebrate communities in rot holes suggests that management of deadwood habitats in woodlands should strive to generate environmental heterogeneity to promote invertebrate diversity. Additional research is required to define how management and conservation activities can further promote enhanced biodiversity across rot holes.
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Affiliation(s)
- Jordan P Cuff
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Fredric M Windsor
- School of Natural and Environmental Science, Newcastle University, Agriculture Building, Newcastle upon Tyne NE1 7RU, UK
| | - Emma C Gilmartin
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
- Woodland Trust, Kempton Way, Grantham, Lincolnshire NG31 6LL, UK
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - T Hefin Jones
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
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12
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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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13
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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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14
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Viotti C, Bach C, Maillard F, Ziegler-Devin I, Mieszkin S, Buée M. Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition. Environ Microbiol 2021; 23:6177-6193. [PMID: 33848050 DOI: 10.1111/1462-2920.15522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.
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Affiliation(s)
- Chloé Viotti
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Cyrille Bach
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - François Maillard
- Department of Plant and Microbial Biology University of Minnesota St. Paul, Saint Paul, Minnesota, 55108, USA
| | | | - Sophie Mieszkin
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
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Sperandio GB, Filho EXF. An overview of Trichoderma reesei co-cultures for the production of lignocellulolytic enzymes. Appl Microbiol Biotechnol 2021; 105:3019-3025. [PMID: 33825000 DOI: 10.1007/s00253-021-11261-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 12/01/2022]
Abstract
Biorefineries are core facilities for implementing a sustainable circular bioeconomy. These facilities rely on microbial enzymes to hydrolyze lignocellulosic substrates into fermentable sugars. Fungal co-cultures mimic the process of natural biodegradation and have been shown to increase certain enzyme activities. Trichoderma reesei and its many mutant strains are major cellulase producers and are heavily utilized as a source of carbohydrate-active enzymes. Several reports have demonstrated that T. reesei co-cultures present higher enzyme activities compared with its monocultures, especially in the context of β-glucosidase activity. The performance of T. reesei during co-culturing has been assessed with several fungal partners, including Aspergillus niger, one of the most recurrent partners. Various aspects of co-cultivation still need further investigation, especially regarding the molecular interactions between fungi in controlled environments and the optimization of the resulting enzyme cocktails. Since plenty of genetic and physiological data on T. reesei is available, the species is an outstanding candidate for future co-culture investigations. Co-cultures are still a developing field for industrial enzyme production, and many aspects of the technique need further improvement before real applications. KEY POINTS: • T. reesei co-cultures are an alternative for producing lignocellulolytic enzymes. • Several reports suggest an increase in certain enzyme activities in co-cultures. • More in-depth investigations of co-cultures are necessary for advancing this field.
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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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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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Zhang C, Lin Z, Que Y, Fallah N, Tayyab M, Li S, Luo J, Zhang Z, Abubakar AY, Zhang H. Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol 2021; 21:52. [PMID: 33596827 PMCID: PMC7890633 DOI: 10.1186/s12866-021-02115-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields. RESULT The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity. CONCLUSIONS Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.
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Affiliation(s)
- Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhaoli Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiyan Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jun Luo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zichu Zhang
- Fuzhou No.8 High School, Fuzhou, 350000 China
| | - Ahmad Yusuf Abubakar
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Holec J, Kučera T. Richness and composition of macrofungi on large decaying trees in a Central European old-growth forest: a case study on silver fir (Abies alba). Mycol Prog 2020. [DOI: 10.1007/s11557-020-01637-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Lee MR, Oberle B, Olivas W, Young DF, Zanne AE. Wood construction more strongly shapes deadwood microbial communities than spatial location over 5 years of decay. Environ Microbiol 2020; 22:4702-4717. [PMID: 32840945 DOI: 10.1111/1462-2920.15212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 07/12/2020] [Accepted: 07/30/2020] [Indexed: 01/18/2023]
Abstract
Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3-98.8% mass loss while decaying in common garden 'rotplots' in a temperate oak-hickory forest in the Ozark Highlands, MO, USA. Communities were isolated from 21 woody species that had been decomposing for 1-5 years in spatially distinct habitats at the landscape scale (top and bottom of watersheds) and within stems (top and bottom of stems). Microbial community structure varied more strongly with wood traits than with spatial locations, mirroring the relative role of these factors on decay rates on the same pieces of wood even after 5 years. Co-occurring fungal and bacterial communities persistently influenced one another independently from their shared environmental conditions. However, the relative influence of wood construction versus spatial locations differed between fungi and bacteria, suggesting that life history characteristics of these clades structure diversity differently across space and time in decomposing wood.
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Affiliation(s)
- Marissa R Lee
- Department of Plant and Microbial Biology, North Carolina State University, Campus Box 7612, Raleigh, NC, 27695, USA
| | - Brad Oberle
- Division of Natural Sciences, New College of Florida, 5800 Bay Shore Rd., Sarasota, FL, 34243, USA
| | - Wendy Olivas
- Department of Biology, University of Missouri, St Louis, MO, 63108, USA
| | - Darcy F Young
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW Suite 6000, Washington, DC, 20052, USA
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW Suite 6000, Washington, DC, 20052, USA
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21
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Saine S, Ovaskainen O, Somervuo P, Abrego N. Data collected by fruit body‐ and DNA‐based survey methods yield consistent species‐to‐species association networks in wood‐inhabiting fungal communities. OIKOS 2020. [DOI: 10.1111/oik.07502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonja Saine
- Dept of Agricultural Sciences, Univ. of Helsinki Finland
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, Univ. of Helsinki Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Univ. of Helsinki Finland
| | - Nerea Abrego
- Dept of Agricultural Sciences, Univ. of Helsinki Finland
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22
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Mali T, Mäki M, Hellén H, Heinonsalo J, Bäck J, Lundell T. Decomposition of spruce wood and release of volatile organic compounds depend on decay type, fungal interactions and enzyme production patterns. FEMS Microbiol Ecol 2020; 95:5554004. [PMID: 31494677 PMCID: PMC6736282 DOI: 10.1093/femsec/fiz135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/22/2019] [Indexed: 01/18/2023] Open
Abstract
Effect of three wood-decaying fungi on decomposition of spruce wood was studied in solid-state cultivation conditions for a period of three months. Two white rot species (Trichaptum abietinum and Phlebia radiata) were challenged by a brown rot species (Fomitopsis pinicola) in varying combinations. Wood decomposition patterns as determined by mass loss, carbon to nitrogen ratio, accumulation of dissolved sugars and release of volatile organic compounds (VOCs) were observed to depend on both fungal combinations and growth time. Similar dependence of fungal species combination, either white or brown rot dominated, was observed for secreted enzyme activities on spruce wood. Fenton chemistry suggesting reduction of Fe3+ to Fe2+ was detected in the presence of F. pinicola, even in co-cultures, together with substantial degradation of wood carbohydrates and accumulation of oxalic acid. Significant correlation was perceived with two enzyme activity patterns (oxidoreductases produced by white rot fungi; hydrolytic enzymes produced by the brown rot fungus) and wood degradation efficiency. Moreover, emission of four signature VOCs clearly grouped the fungal combinations. Our results indicate that fungal decay type, either brown or white rot, determines the loss of wood mass and decomposition of polysaccharides as well as the pattern of VOCs released upon fungal growth on spruce wood.
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Affiliation(s)
- Tuulia Mali
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
| | - Mari Mäki
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Heidi Hellén
- Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jussi Heinonsalo
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland.,Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jaana Bäck
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
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23
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Vivelo S, Bhatnagar JM. An evolutionary signal to fungal succession during plant litter decay. FEMS Microbiol Ecol 2020; 95:5565043. [PMID: 31574146 PMCID: PMC6772037 DOI: 10.1093/femsec/fiz145] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Ecologists have frequently observed a pattern of fungal succession during litter decomposition, wherein different fungal taxa dominate different stages of decay in individual ecosystems. However, it is unclear which biological features of fungi give rise to this pattern. We tested a longstanding hypothesis that fungal succession depends on the evolutionary history of species, such that different fungal phyla prefer different decay stages. To test this hypothesis, we performed a meta-analysis across studies in 22 different ecosystem types to synthesize fungal decomposer abundances at early, middle and late stages of plant litter decay. Fungal phyla varied in relative abundance throughout decay, with fungi in the Ascomycota reaching highest relative abundance during early stages of decay (P < 0.001) and fungi in the Zygomycota reaching highest relative abundance during late stages of decay (P < 0.001). The best multiple regression model to explain variation in abundance of these fungal phyla during decay included decay stage, as well as plant litter type and climate factors. Most variation in decay-stage preference of fungal taxa was observed at basal taxonomic levels (phylum and class) rather than finer taxonomic levels (e.g. genus). For many finer-scale taxonomic groups and functional groups of fungi, plant litter type and climate factors were better correlates with relative abundance than decay stage per se, suggesting that the patchiness of fungal community composition in space is related to both resource and climate niches of different fungal taxa. Our study indicates that decomposer fungal succession is partially rooted in fungal decomposers’ deep evolutionary history, traceable to the divergence among phyla.
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Affiliation(s)
- Sasha Vivelo
- Dept. of Biology, Boston University, Boston, MA 02215, USA
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24
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Han Z, Zhang L, Jiang Y, Wang H, Jiguet F. Unravelling species co‐occurrence in a steppe bird community of Inner Mongolia: Insights for the conservation of the endangered Jankowski’s Bunting. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Zheng Han
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics School of Life Sciences Northeast Normal University Changchun China
- CESCO UMR7204 MNHN‐CNRS‐Sorbonne Université, CP135 Paris France
| | - Lishi Zhang
- Animal’s Scientific and Technological Institute Agricultural University of Jilin Changchun China
| | - Yunlei Jiang
- Animal’s Scientific and Technological Institute Agricultural University of Jilin Changchun China
| | - Haitao Wang
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics School of Life Sciences Northeast Normal University Changchun China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization School of Life Sciences Northeast Normal University Changchun China
| | - Frédéric Jiguet
- CESCO UMR7204 MNHN‐CNRS‐Sorbonne Université, CP135 Paris France
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25
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Shirouzu T, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K. Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Sci Rep 2020; 10:3057. [PMID: 32080243 PMCID: PMC7033186 DOI: 10.1038/s41598-020-59620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/03/2020] [Indexed: 11/28/2022] Open
Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
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Affiliation(s)
- Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Nobuaki Nagata
- Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Ibaraki, 305-0005, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
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26
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Macrofungi on large decaying spruce trunks in a Central European old-growth forest: what factors affect their species richness and composition? Mycol Prog 2020. [DOI: 10.1007/s11557-019-01541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Norberg A, Halme P, Kotiaho JS, Toivanen T, Ovaskainen O. Experimentally induced community assembly of polypores reveals the importance of both environmental filtering and assembly history. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Torres-Andrade P, Morrell JJ, Cappellazzi J, Stone JK. Culture-based identification to examine spatiotemporal patterns of fungal communities colonizing wood in ground contact. Mycologia 2019; 111:703-718. [PMID: 31348726 DOI: 10.1080/00275514.2019.1631050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Timber durability is often assessed using small wood stakes exposed in direct soil contact, and the assessment generally emphasizes effects on wood rather than organisms involved. Understanding fungal colonization patterns can help identify key decay agents under varying conditions and use these patterns to improve wood protection strategies. Fungal colonization of red alder (Alnus rubra), Douglas-fir (Pseudotsuga menziesii) heartwood/sapwood, and western redcedar (Thuja plicata) field stakes was assessed over 2 y in western Oregon. Spatiotemporal fungal community variations were identified via culturing and DNA sequencing, where 814 isolates were identified from 84 stakes. Forty-six ascomycete genera were identified, with Phialophora, Trichoderma, and Epicoccum species occurring most frequently. Twenty-three basidiomycete genera were identified, with Trametes and Phanerochaete being the most common. Douglas-fir and western redcedar stakes contained the highest and lowest diversity levels, respectively, reflecting natural durability differences of these species. Fungal species abundance was higher below ground than in the above ground and groundline zones, likely reflecting more stable moisture regimes, proximity to soil-based fungi, and potential nutrient migration into wood beneath the soil surface. Ascomycetes were proportionally more abundant early in the exposure period, but basidiomycetes were also observed early in the process, and there appeared to be no consistent colonization pattern.
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Affiliation(s)
- Paola Torres-Andrade
- Department of Wood Science & Engineering, Oregon State University , Corvallis , Oregon 97330
| | - Jeffrey J Morrell
- Centre for Timber Durability and Design Life, University of the Sunshine Coast , Brisbane , Australia
| | - Jed Cappellazzi
- Department of Wood Science & Engineering, Oregon State University , Corvallis , Oregon 97330
| | - Jeffrey K Stone
- Department of Botany and Plant Pathology, Oregon State University , Corvallis , Oregon 97330
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29
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Consistent trade-offs in fungal trait expression across broad spatial scales. Nat Microbiol 2019; 4:846-853. [DOI: 10.1038/s41564-019-0361-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/06/2019] [Indexed: 12/27/2022]
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30
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Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes. Appl Environ Microbiol 2018; 84:AEM.01133-18. [PMID: 30097442 DOI: 10.1128/aem.01133-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/04/2018] [Indexed: 11/20/2022] Open
Abstract
Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.
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31
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Jacobsen RM, Sverdrup‐Thygeson A, Kauserud H, Mundra S, Birkemoe T. Exclusion of invertebrates influences saprotrophic fungal community and wood decay rate in an experimental field study. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13196] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rannveig M. Jacobsen
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
- The Norwegian Institute for Nature Research Oslo Norway
| | - Anne Sverdrup‐Thygeson
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Tone Birkemoe
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
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32
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Loyd AL, Held BW, Linder ER, Smith JA, Blanchette RA. Elucidating wood decomposition by four species of Ganoderma from the United States. Fungal Biol 2018; 122:254-263. [DOI: 10.1016/j.funbio.2018.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 10/18/2022]
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33
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Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol 2018; 15:197-205. [PMID: 29362469 PMCID: PMC6813786 DOI: 10.1038/nrgastro.2017.173] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.
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Affiliation(s)
- Daniel Sprockett
- Department of Microbiology and Immunology, Stanford University School ofMedicine, 291 Campus Drive, Stanford, California 94305, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, California 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School ofMedicine, 291 Campus Drive, Stanford, California 94305, USA
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304, USA
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34
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Abstract
Understanding the mechanisms underlying wood decay basidiomycete community dynamics is crucial for fully understanding decomposition processes, and for modelling ecosystem function and resilience to environmental change. Competition drives community development in decaying woody resources, with interactions occurring at a distance, following physical contact, and through specialised relationships such as mycoparasitism. Outcomes of combative interactions range from replacement, where one mycelium displaces another, to deadlock, where neither combatant captures territory from the other; and a spectrum of intermediate outcomes (i.e. partial or mutual replacement) lie between these extremes. Many wood decay basidiomycetes coexist within a resource, in a complex and dynamic community, and new research techniques are focussing on spatial orientation of interactions in 3 dimensions, as opposed to historical two-dimensional research. Not only do interactions drive changes in species composition and thus wood decomposition rate, they also may have industrial applications in biocontrol of pathogenic or nuisance fungi, enzyme production, and in the production of novel antifungals and antibiotics. Altogether, fungal interactions are a fascinating and important field of study.
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35
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Maynard DS, Covey KR, Crowther TW, Sokol NW, Morrison EW, Frey SD, van Diepen LTA, Bradford MA. Species associations overwhelm abiotic conditions to dictate the structure and function of wood‐decay fungal communities. Ecology 2018; 99:801-811. [DOI: 10.1002/ecy.2165] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/02/2017] [Accepted: 01/08/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Daniel S. Maynard
- Department of Ecology and Evolution University of Chicago 1101 E 57th Street Chicago Illinois 60637 USA
- School of Forestry and Environmental Studies Yale University 370 Prospect Street New Haven Connecticut 06511 USA
| | - Kristofer R. Covey
- School of Forestry and Environmental Studies Yale University 370 Prospect Street New Haven Connecticut 06511 USA
| | - Thomas W. Crowther
- Institute of Integrative Biology ETH Zurich Univeritätstrasse 16 8006 Zurich Switzerland
| | - Noah W. Sokol
- School of Forestry and Environmental Studies Yale University 370 Prospect Street New Haven Connecticut 06511 USA
| | - Eric W. Morrison
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire 03824 USA
| | - Serita D. Frey
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire 03824 USA
| | - Linda T. A. van Diepen
- Department of Ecosystem Science and Management University of Wyoming 1000 East University Avenue Laramie Wyoming 82071 USA
| | - Mark A. Bradford
- School of Forestry and Environmental Studies Yale University 370 Prospect Street New Haven Connecticut 06511 USA
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36
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Rummens K, De Meester L, Souffreau C. Inoculation history affects community composition in experimental freshwater bacterioplankton communities. Environ Microbiol 2018; 20:1120-1133. [DOI: 10.1111/1462-2920.14053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/15/2018] [Accepted: 01/21/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Koen Rummens
- Laboratory of Aquatic Ecology, Evolution & Conservation; KU Leuven, Charles Deberiotstraat 32; 3000 Leuven Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution & Conservation; KU Leuven, Charles Deberiotstraat 32; 3000 Leuven Belgium
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution & Conservation; KU Leuven, Charles Deberiotstraat 32; 3000 Leuven Belgium
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37
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Mali T, Kuuskeri J, Shah F, Lundell TK. Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes. PLoS One 2017; 12:e0185171. [PMID: 28953947 PMCID: PMC5617175 DOI: 10.1371/journal.pone.0185171] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.
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Affiliation(s)
- Tuulia Mali
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Firoz Shah
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Taina Kristina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
- * E-mail:
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38
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Mäkipää R, Rajala T, Schigel D, Rinne KT, Pennanen T, Abrego N, Ovaskainen O. Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs. THE ISME JOURNAL 2017; 11:1964-1974. [PMID: 28430188 PMCID: PMC5563949 DOI: 10.1038/ismej.2017.57] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 11/25/2022]
Abstract
We investigated the interaction between fungal communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the fungal communities from soil, some fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting fungal communities interact at all decay phases of wood that has important implications in fungal community dynamics and thus nutrient transportation.
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Affiliation(s)
- Raisa Mäkipää
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tiina Rajala
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Dmitry Schigel
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Katja T Rinne
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Taina Pennanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Nerea Abrego
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Otso Ovaskainen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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Abstract
Decomposer fungi continually deplete the organic resources they inhabit, so successful colonization of new resources is a crucial part of their ecology. Colonization success can be split into (i) the ability to arrive at, gain entry into, and establish within a resource and (ii) the ability to persist within the resource until reproduction and dissemination. Fungi vary in their life history strategies, the three main drivers of which are stress (S-selected), disturbance (ruderal, or R-selected), and incidence of competitors (C-selected); however, fungi often have combinations of characteristics from different strategies. Arrival at a new resource may occur as spores or mycelium, with successful entry and establishment (primary resource capture) within the resource largely dependent on the enzymatic ability of the fungus. The communities that develop in a newly available resource depend on environmental conditions and, in particular, the levels of abiotic stress present (e.g., high temperature, low water availability). Community change occurs when these initial colonizers are replaced by species that are either more combative (secondary resource capture) or better able to tolerate conditions within the resource, either through changing abiotic conditions or due to modification of the resource by the initial colonizers. Competition for territory may involve highly specialized species-specific interactions such as mycoparasitism or may be more general; in both cases combat involves changes in morphology, metabolism, and reactive oxygen species production, and outcomes of these interactions can be altered under different environmental conditions. In summary, community development is not a simple ordered sequence, but a complex ever-changing mosaic.
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Leopold DR, Wilkie JP, Dickie IA, Allen RB, Buchanan PK, Fukami T. Priority effects are interactively regulated by top‐down and bottom‐up forces: evidence from wood decomposer communities. Ecol Lett 2017; 20:1054-1063. [DOI: 10.1111/ele.12803] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/26/2017] [Accepted: 06/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Ian A. Dickie
- BioProtection Research Centre Lincoln University Lincoln7647 New Zealand
- University of Canterbury School of Biological Sciences Christchurch8140 New Zealand
| | | | | | - Tadashi Fukami
- Department of Biology Stanford University Stanford CA94305 USA
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Mair L, Harrison PJ, Räty M, Bärring L, Strandberg G, Snäll T. Forest management could counteract distribution retractions forced by climate change. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:1485-1497. [PMID: 28370800 DOI: 10.1002/eap.1541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Climate change is expected to drive the distribution retraction of northern species. However, particularly in regions with a history of intensive exploitation, changes in habitat management could facilitate distribution expansions counter to expectations under climate change. Here, we test the potential for future forest management to facilitate the southward expansion of an old-forest species from the boreal region into the boreo-nemoral region, contrary to expectations under climate change. We used an ensemble of species distribution models based on citizen science data to project the response of Phellinus ferrugineofuscus, a red-listed old-growth indicator, wood-decaying fungus, to six forest management and climate change scenarios. We projected change in habitat suitability across the boreal and boreo-nemoral regions of Sweden for the period 2020-2100. Scenarios varied in the proportion of forest set aside from production, the level of timber extraction, and the magnitude of climate change. Habitat suitabilities for the study species were projected to show larger relative increases over time in the boreo-nemoral region compared to the boreal region, under all scenarios. By 2100, mean suitabilities in set-aside forest in the boreo-nemoral region were similar to the suitabilities projected for set-aside forest in the boreal region in 2020, suggesting that occurrence in the boreo-nemoral region could be increased. However, across all scenarios, consistently higher projected suitabilities in set-aside forest in the boreal region indicated that the boreal region remained the species stronghold. Furthermore, negative effects of climate change were evident in the boreal region, and projections suggested that climatic changes may eventually counteract the positive effects of forest management in the boreo-nemoral region. Our results suggest that the current rarity of this old-growth indicator species in the boreo-nemoral region may be due to the history of intensive forestry. Forest management therefore has the potential to compensate for the negative effects of climate change. However, increased occurrence at the southern range edge would depend on the dispersal and colonization ability of the species. An increase in the amount of set-aside forest across both the boreal and boreo-nemoral regions is therefore likely to be required to prevent the decline of old-forest species under climate change.
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Affiliation(s)
- Louise Mair
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), P.O. Box 7007, SE-75007, Uppsala, Sweden
| | - Philip J Harrison
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), P.O. Box 7007, SE-75007, Uppsala, Sweden
| | - Minna Räty
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), P.O. Box 7007, SE-75007, Uppsala, Sweden
| | - Lars Bärring
- Rossby Centre, Swedish Meteorological and Hydrological Institute (SMHI), SE-60176, Norrköping, Sweden
| | - Gustav Strandberg
- Rossby Centre, Swedish Meteorological and Hydrological Institute (SMHI), SE-60176, Norrköping, Sweden
| | - Tord Snäll
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), P.O. Box 7007, SE-75007, Uppsala, Sweden
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Boddy L, Hiscox J, Gilmartin EC, Johnston SR, Heilmann-Clausen J. Chapter 12 Wood Decay Communities in Angiosperm Wood. Mycology 2017. [DOI: 10.1201/9781315119496-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Pec GJ, Karst J, Taylor DL, Cigan PW, Erbilgin N, Cooke JEK, Simard SW, Cahill JF. Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak. THE NEW PHYTOLOGIST 2017; 213:864-873. [PMID: 27659418 DOI: 10.1111/nph.14195] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi.
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Affiliation(s)
- Gregory J Pec
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
| | - Justine Karst
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - D Lee Taylor
- Department of Biology, University of New Mexico, Castetter Hall 104, Albuquerque, NM, 87131, USA
| | - Paul W Cigan
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, University of British Columbia, Forest Sciences Centre #3601-2424 Main Hall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
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Yamashita S, Hirose D. Phylogenetic analysis of Ganoderma australe complex in a Bornean tropical rainforest and implications for mechanism of coexistence of various phylogenetic types. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Ruete A, Snäll T, Jonsson BG, Jönsson M. Contrasting long-term effects of transient anthropogenic edges and forest fragment size on generalist and specialist deadwood-dwelling fungi. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12835] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alejandro Ruete
- Ecology Department; Swedish University of Agricultural Sciences (SLU); SE-750 07 Uppsala Sweden
| | - Tord Snäll
- Swedish Species Information Centre; SLU; SE-750 07 Uppsala Sweden
| | - Bengt Gunnar Jonsson
- Department of Natural Sciences; Mid Sweden University; Sundsvall SE-851 70 Sweden
| | - Mari Jönsson
- Swedish Species Information Centre; SLU; SE-750 07 Uppsala Sweden
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47
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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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48
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Wal A, Klein Gunnewiek PJA, Cornelissen JHC, Crowther TW, Boer W. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. Ecosphere 2016. [DOI: 10.1002/ecs2.1393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Annemieke Wal
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
| | - Paulien J. A. Klein Gunnewiek
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
| | - J. Hans C. Cornelissen
- Systems Ecology, Department of Ecological ScienceVU University (Vrije Universiteit) Amsterdam De Boelelaan 1085 1081 HV Amsterdam The Netherlands
| | - Thomas W. Crowther
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6700 AB Wageningen The Netherlands
| | - Wietse Boer
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
- Department of Soil QualityWageningen University Droevendaalsesteeg 4, Building 104 6708 PB Wageningen The Netherlands
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Ruete A, Snäll T, Jönsson M. Dynamic anthropogenic edge effects on the distribution and diversity of fungi in fragmented old-growth forests. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:1475-1485. [PMID: 27755761 DOI: 10.1890/15-1271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/19/2015] [Accepted: 12/01/2015] [Indexed: 06/06/2023]
Abstract
Diversity patterns and dynamics at forest edges are not well understood. We disentangle the relative importance of edge-effect variables on spatio-temporal patterns in species richness and occupancy of deadwood-dwelling fungi in fragmented old-growth forests. We related richness and log occupancy by 10 old-growth forest indicator fungi and by two common fungi to log conditions in natural and anthropogenic edge habitats of 31 old-growth Picea abies forest stands in central Sweden. We compared edge-to-interior gradients (100 m) to the forest interior (beyond 100 m), and we analyzed stand-level changes after 10 yr. Both richness and occupancy of logs by indicator species was negatively related to adjacent young clear-cut edges, but this effect decreased with increasing clear-cut age. The occupancy of logs by indicator species also increased with increasing distance to the natural edges. In contrast, the occupancy of logs by common species was positively related or unrelated to distance to clear-cut edges regardless of the edge age, and this was partly explained by fungal specificity to substrate quality. Stand-level mean richness and mean occupancy of logs did not change for indicator or common species over a decade. By illustrating the importance of spatial and temporal dimensions of edge effects, we extend the general understanding of the distribution and diversity of substrate-confined fungi in fragmented old-growth forests. Our results highlight the importance of longer forest rotation times adjacent to small protected areas and forest set-asides, where it may take more than 50 yr for indicator species richness levels to recover to occupancy levels observed in the forest interior. Also, non-simultaneous clear-cutting of surrounding productive forests in a way that reduces the edge effect over time (i.e., dynamic buffers) may increase the effective core area of small forest set-asides and improve their performance on protecting species of special concern for conservation.
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Affiliation(s)
- Alejandro Ruete
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), PO 7007, Uppsala, SE-750 07, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), PO 7007, Uppsala, SE-750 07, Sweden
| | - Tord Snäll
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), PO 7007, Uppsala, SE-750 07, Sweden
| | - Mari Jönsson
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), PO 7007, Uppsala, SE-750 07, Sweden
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Abrego N, Halme P, Purhonen J, Ovaskainen O. Fruit body based inventories in wood-inhabiting fungi: Should we replicate in space or time? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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