1
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Simpson HJ, Andrew C, Skrede I, Kauserud H, Schilling JS. Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates. THE NEW PHYTOLOGIST 2024; 242:2775-2786. [PMID: 38567688 DOI: 10.1111/nph.19723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.
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Affiliation(s)
- Hunter J Simpson
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN, 55108, USA
| | - Carrie Andrew
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
- Natural History Museum, University of Oslo, Sars' gate 1, 0562, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316, Oslo, Norway
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2
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Lunde LF, Jacobsen R, Kauserud H, Boddy L, Nybakken L, Sverdrup-Thygeson A, Birkemoe T. Legacies of invertebrate exclusion and tree secondary metabolites control fungal communities in dead wood. Mol Ecol 2022; 31:3241-3253. [PMID: 35363919 PMCID: PMC9322270 DOI: 10.1111/mec.16448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
Abstract
During decomposition of organic matter, microbial communities may follow different successional trajectories depending on the initial environment and colonizers. The timing and order of the species arrival (assembly history) can lead to divergent communities through priority effects. We explored how assembly history and resource quality affected fungal communities and decay rate of decomposing wood, 1.5 and 4.5 years after tree felling. Additionally, we investigated the effect of invertebrate exclusion during the first two summers. We measured initial resource quality of bark and wood of aspen (Populus tremula) logs and surveyed the fungal communities by DNA metabarcoding at different times during succession. We found that gradients in fungal community composition were related to resource quality and discuss how this may reflect different fungal life history strategies. As with previous studies, the initial amount of bark tannins was negatively correlated with wood decomposition rate over 4.5 years. The initial fungal community explained variation in community composition after 1.5, but not 4.5 years, of succession. Although the assembly history of initial colonizers may cause alternate trajectories in successional communities, our results indicate that the communities may converge with the arrival of secondary colonizers. We also identified a strong legacy of invertebrate exclusion on fungal communities, even after 4.5 years of succession, thereby adding crucial knowledge on the importance of invertebrates in affecting fungal community development. By measuring and manipulating aspects of assembly history and resource quality that have rarely been studied, we expand our understanding of the complexity of fungal community dynamics.
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Affiliation(s)
- Lisa Fagerli Lunde
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Rannveig Jacobsen
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway.,Norwegian Institute for Nature Research (NINA), 0855, Oslo, Norway
| | - Håvard Kauserud
- University of Oslo, Section for Genetics and Evolutionary Biology (EVOGENE), 0316, Oslo, Norway
| | - Lynne Boddy
- Cardiff University, School of Biosciences, Cardiff, UK
| | - Line Nybakken
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Anne Sverdrup-Thygeson
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Tone Birkemoe
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
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3
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Yang S, Poorter L, Kuramae EE, Sass-Klaassen U, Leite MFA, Costa OYA, Kowalchuk GA, Cornelissen JHC, van Hal J, Goudzwaard L, Hefting MM, van Logtestijn RSP, Sterck FJ. Stem traits, compartments, and tree species affect fungal communities on decaying wood. Environ Microbiol 2022; 24:3625-3639. [PMID: 35229433 PMCID: PMC9544286 DOI: 10.1111/1462-2920.15953] [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: 10/03/2021] [Revised: 01/12/2022] [Accepted: 02/23/2022] [Indexed: 12/01/2022]
Abstract
Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.
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Affiliation(s)
- Shanshan Yang
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ute Sass-Klaassen
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Jurgen van Hal
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Leo Goudzwaard
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Richard S P van Logtestijn
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Frank J Sterck
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
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4
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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5
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Clocchiatti A, Hannula SE, Hundscheid MPJ, Klein Gunnewiek PJA, de Boer W. Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings. Environ Microbiol 2021; 23:6056-6073. [PMID: 33973345 PMCID: PMC8596668 DOI: 10.1111/1462-2920.15563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/05/2021] [Indexed: 11/28/2022]
Abstract
Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes.
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Affiliation(s)
- Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
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6
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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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7
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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8
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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9
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Purahong W, Pietsch KA, Bruelheide H, Wirth C, Buscot F, Wubet T. Potential links between wood-inhabiting and soil fungal communities: Evidence from high-throughput sequencing. Microbiologyopen 2019; 8:e00856. [PMID: 31134764 PMCID: PMC6741142 DOI: 10.1002/mbo3.856] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/23/2022] Open
Abstract
Wood‐inhabiting fungi (WIF) are pivotal to wood decomposition, which in turn strongly influences nutrient dynamics in forest soils. However, their dispersal mechanisms remain unclear. We hypothesized that the majority of WIF are soil‐borne. For this reason, the presented research aimed to quantify the contribution of soil as a source and medium for the dispersal of WIF to deadwood using high‐throughput sequencing. We tested effects of tree species (specifically Schima superba and Pinus massoniana) on the percentage of WIF shared between soil and deadwood in a Chinese subtropical forest ecosystem. We also assessed the taxonomic and ecological functional group affiliations of the fungal community shared between soil and deadwood. Our results indicate that soil is a major route for WIF colonization as 12%–15% (depending on the tree species) of soil fungi were simultaneously detected in deadwood. We also demonstrate that tree species (p < 0.01) significantly shapes the composition of the shared soil and deadwood fungal community. The pH of decomposing wood was shown to significantly correspond (p < 0.01) with the shared community of wood‐inhabiting (of both studied tree species) and soil fungi. Furthermore, our data suggest that a wide range of fungal taxonomic (Rozellida, Zygomycota, Ascomycota, and Basidiomycota) and ecological functional groups (saprotrophs, ectomycorrhizal, mycoparasites, and plant pathogens) may use soil as a source and medium for transport to deadwood in subtropical forest ecosystem. While 12%–62% of saprotrophic, ectomycorrhizal, and mycoparasitic WIF may utilize soil to colonize deadwood, only 5% of the detected plant pathogens were detected in both soil and deadwood, implying that these fungi use other dispersal routes. Animal endosymbionts and lichenized WIF were not detected in the soil samples. Future studies should consider assessing the relative contributions of other possible dispersal mechanisms (e.g. wind, water splash, water dispersal, animal dispersal, and mycelial network) in the colonization of deadwood by soil fungi.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Katherina A Pietsch
- Department of Systematic Botany and Functional Biodiversity, Leipzig University, Leipzig, Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian Wirth
- Department of Systematic Botany and Functional Biodiversity, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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10
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Chan JY, Bonser SP, Powell JR, Cornwell WK. When to cut your losses: Dispersal allocation in an asexual filamentous fungus in response to competition. Ecol Evol 2019; 9:4129-4137. [PMID: 31015993 PMCID: PMC6467841 DOI: 10.1002/ece3.5041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 11/12/2022] Open
Abstract
Fungal communities often form on ephemeral substrates and dispersal is critical for the persistence of fungi among the islands that form these metacommunities. Within each substrate, competition for space and resources is vital for the local persistence of fungi. The capacity to detect and respond by dispersal away from unfavorable conditions may confer higher fitness in fungi. Informed dispersal theory posits that organisms are predicted to detect information about their surroundings which may trigger a dispersal response. As such, we expect that fungi will increase allocation to dispersal in the presence of a strong competitor.In a laboratory setting, we tested how competition with other filamentous fungi affected the development of conidial pycnidiomata (asexual fruiting bodies) in Phacidium lacerum over 10 days. Phacidium lacerum was not observed to produce more asexual fruiting bodies or produce them earlier when experiencing interspecific competition with other filamentous fungi. However, we found that a trade-off existed between growth rate and allocation to dispersal. We also observed a defensive response to specific interspecific competitors in the form of hyphal melanization of the colony which may have an impact on the growth rate and dispersal trade-off.Our results suggest that P. lacerum have the capacity to detect and respond to competitors by changing their allocation to dispersal and growth. However, allocation to defence may come at a cost to growth and dispersal. Thus, it is likely that optimal life history allocation in fungi constrained to ephemeral resources will depend on the competitive strength of neighbors surrounding them.
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Affiliation(s)
- Justin Y. Chan
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Stephen P. Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Jeff R. Powell
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
| | - William K. Cornwell
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNSWAustralia
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11
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Leonhardt S, Hoppe B, Stengel E, Noll L, Moll J, Bässler C, Dahl A, Buscot F, Hofrichter M, Kellner H. Molecular fungal community and its decomposition activity in sapwood and heartwood of 13 temperate European tree species. PLoS One 2019; 14:e0212120. [PMID: 30763365 PMCID: PMC6375594 DOI: 10.1371/journal.pone.0212120] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/28/2019] [Indexed: 12/27/2022] Open
Abstract
Deadwood is an important structural component in forest ecosystems and plays a significant role in global carbon and nutrient cycling. Relatively little is known about the formation and decomposition of CWD by microbial communities in situ and about the factors controlling the associated processes. In this study, we intensively analyzed the molecular fungal community composition and species richness in relation to extracellular enzyme activity and differences in decomposing sapwood and heartwood of 13 temperate tree species (four coniferous and nine deciduous species, log diameter 30–40 cm and 4 m long) in an artificial experiment involving placing the logs on the forest soil for six years. We observed strong differences in the molecular fungal community composition and richness among the 13 tree species, and specifically between deciduous and coniferous wood, but unexpectedly no difference was found between sapwood and heartwood. Fungal species richness correlated positively with wood extractives and negatively with fungal biomass. A distinct fungal community secreting lignocellulolytic key enzymes seemed to dominate the decomposition of the logs in this specific phase. In particular, the relative sequence abundance of basidiomycetous species of the Meruliaceae (e.g. Bjerkandera adusta) correlated with ligninolytic manganese peroxidase activity. Moreover, this study reveals abundant white-rot causing Basidiomycota and soft-rot causing Ascomycota during this phase of wood decomposition.
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Affiliation(s)
- Sabrina Leonhardt
- Technische Universität Dresden, International Institute Zittau, Department of Bio- and Environmental Sciences, Zittau, Germany
- * E-mail:
| | - Björn Hoppe
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Julius Kuehn-Institute, Institute for National and International Plant Health, Braunschweig, Germany
| | - Elisa Stengel
- University of Würzburg, Field Station Fabrikschleichach, Rauhenebrach, Germany
| | - Lisa Noll
- University of Vienna, Department of Microbiology and Ecosystem Science, Vienna, Austria
| | - Julia Moll
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | | | - Andreas Dahl
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering, CMCB Technology Platform, Deep Sequencing Group, Dresden, Germany
| | - Francois Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Martin Hofrichter
- Technische Universität Dresden, International Institute Zittau, Department of Bio- and Environmental Sciences, Zittau, Germany
| | - Harald Kellner
- Technische Universität Dresden, International Institute Zittau, Department of Bio- and Environmental Sciences, Zittau, Germany
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12
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13
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van der Wal A, klein Gunnewiek P, de Boer W. Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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