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Bielčik M, Schlägel UE, Schäfer M, Aguilar-Trigueros CA, Lakovic M, Sosa-Hernández MA, Hammer EC, Jeltsch F, Rillig MC. Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence. Biol Rev Camb Philos Soc 2024. [PMID: 39073180 DOI: 10.1111/brv.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.
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Affiliation(s)
- Miloš Bielčik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str.84, Müncheberg, 15374, Germany
| | - Ulrike E Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Merlin Schäfer
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
- Federal Agency for Nature Conservation, Alte Messe 6, Leipzig, 04103, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Building R2, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Seminaarinkatu 15, Jyväskylä, 40014, Finland
| | - Milica Lakovic
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Moisés A Sosa-Hernández
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Edith C Hammer
- Department of Biology, Microbial Ecology, Lund University, Ekologihuset, Sölvegatan 37, Lund, 22362, Sweden
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
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Li T, Liu Y, Zhu H, Cao L, Zhou Y, Liu D, Shen Q. Cellular ATP redistribution achieved by deleting Tgparp improves lignocellulose utilization of Trichoderma under heat stress. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:54. [PMID: 38637859 PMCID: PMC11027231 DOI: 10.1186/s13068-024-02502-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Thermotolerance is widely acknowledged as a pivotal factor for fungal survival across diverse habitats. Heat stress induces a cascade of disruptions in various life processes, especially in the acquisition of carbon sources, while the mechanisms by which filamentous fungi adapt to heat stress and maintain carbon sources are still not fully understood. RESULTS Using Trichoderma guizhouense, a representative beneficial microorganism for plants, we discover that heat stress severely inhibits the lignocellulases secretion, affecting carbon source utilization efficiency. Proteomic results at different temperatures suggest that proteins involved in the poly ADP-ribosylation pathway (TgPARP and TgADPRase) may play pivotal roles in thermal adaptation and lignocellulose utilization. TgPARP is induced by heat stress, while the deletion of Tgparp significantly improves the lignocellulose utilization capacity and lignocellulases secretion in T. guizhouense. Simultaneously, the absence of Tgparp prevents the excessive depletion of ATP and NAD+, enhances the protective role of mitochondrial membrane potential (MMP), and elevates the expression levels of the unfolded protein response (UPR)-related regulatory factor Tgire. Further investigations reveal that a stable MMP can establish energy homeostasis, allocating more ATP within the endoplasmic reticulum (ER) to reduce protein accumulation in the ER, thereby enhancing the lignocellulases secretion in T. guizhouense under heat stress. CONCLUSIONS Overall, these findings underscored the significance of Tgparp as pivotal regulators in lignocellulose utilization under heat stress and provided further insights into the molecular mechanism of filamentous fungi in utilizing lignocellulose.
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Affiliation(s)
- Tuo Li
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yang Liu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Han Zhu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Linhua Cao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yihao Zhou
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dongyang Liu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China.
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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3
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Perreault L, Forrester JA, Lindner DL, Jusino MA, Fraver S, Banik MT, Mladenoff DJ. Linking wood-decay fungal communities to decay rates: Using a long-term experimental manipulation of deadwood and canopy gaps. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Mycelium-Composite Materials-A Promising Alternative to Plastics? J Fungi (Basel) 2023; 9:jof9020210. [PMID: 36836324 PMCID: PMC9965147 DOI: 10.3390/jof9020210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Plastic waste inefficiently recycled poses a major environmental concern attracting attention from both civil society and decision makers. Counteracting the phenomenon is an important challenge today. New possibilities are being explored to find alternatives to plastics, and one of them refers to mycelium-composite materials (MCM). Our study aimed at investigating the possibility of using wood and litter inhabiting basidiomycetes, an underexplored group of fungi that grow fast and create strong mycelial mats, to produce biodegradable materials with valuable properties, using cheap by-products as a substrate for growth. Seventy-five strains have been tested for their ability to grow on low-nutrient media and to form compact mycelial mats. Eight strains were selected further for evaluation on several raw substrates for producing in vitro myco-composites. The physico-mechanical properties of these materials, such as firmness, elasticity and impermeability, were analyzed. Abortiporus biennis RECOSOL73 was selected to obtain, at the laboratory scale, a real biodegradable product. Our results suggest that the strain used is a promising candidate with real possibilities for scalability. Finally, corroborating our results with scientific available data, discussions are being made over the feasibility of such technology, cost-effectiveness, scalability, availability of raw materials and, not least, where future studies should be directed to.
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Jomura M, Yoshida R, Michalčíková L, Tláskal V, Baldrian P. Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe. J Fungi (Basel) 2022; 8:jof8070673. [PMID: 35887430 PMCID: PMC9325057 DOI: 10.3390/jof8070673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Dead wood represents an important pool of carbon and nitrogen in forest ecosystems. This source of soil organic matter has diverse ecosystem functions that include, among others, carbon and nitrogen cycling. However, information is limited on how deadwood properties such as chemical composition, decomposer abundance, community composition, and age correlate and affect decomposition rate. Here, we targeted coarse dead wood of beech, spruce, and fir, namely snags and tree trunks (logs) in an old-growth temperate forest in central Europe; measured their decomposition rate as CO2 production in situ; and analyzed their relationships with other measured variables. Respiration rate of dead wood showed strong positive correlation with acid phosphatase activity and negative correlation with lignin content. Fungal biomass (ergosterol content) and moisture content were additional predictors. Our results indicate that dead wood traits, including tree species, age, and position (downed/standing), affected dead wood chemical properties, microbial biomass, moisture condition, and enzyme activity through changes in fungal communities and ultimately influenced the decomposition rate of dead wood.
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Affiliation(s)
- Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
- Correspondence:
| | - Riki Yoshida
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
| | - Lenka Michalčíková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
- Department of Biology, Faculty of Science, University of Hradec Kralove, Hradecká 1285, 500-03 Hradec Králové, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
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6
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Fukasawa Y, Kaga K. Surface Area of Wood Influences the Effects of Fungal Interspecific Interaction on Wood Decomposition—A Case Study Based on Pinus densiflora and Selected White Rot Fungi. J Fungi (Basel) 2022; 8:jof8050517. [PMID: 35628772 PMCID: PMC9145481 DOI: 10.3390/jof8050517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Wood decomposer basidiomycetes are the major agents of lignocellulose decomposition in dead wood. As their interspecific interaction affects wood decomposition, difference in interaction area may alter the magnitude of the effects. This study examines the effects of wood surface area on decomposition by interacting basidiomycetes using laboratory incubation experiments with pine sapwood as a model. Two types of pine wood blocks with equal volume but identical surface area were prepared for colonization by one of four white rot basidiomycete species. The colonized wood blocks were then placed on agar media already colonized by the same strain or one of the other species, simulating fungal monoculture and interspecific interactions on wood surface. Results demonstrated that the decay rate of wood was greater in wood with larger surface, and wood decay was accelerated by the interaction of two fungal species in wood with larger surface but not in wood with smaller surface. In contrast, lignin decomposition was influenced by the competitor in wood with smaller surface but not in wood with larger surface. These results suggest that the observed promotion of decay by fungal interspecific interaction might not be attributable to the resource partitioning between fungal species but to the accelerated carbon of competition cost compensation in this case.
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7
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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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8
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Effect of ligninolytic axenic and coculture white-rot fungi on rice straw chemical composition and in vitro fermentation characteristics. Sci Rep 2022; 12:1129. [PMID: 35064211 PMCID: PMC8782829 DOI: 10.1038/s41598-022-05107-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/06/2022] [Indexed: 01/19/2023] Open
Abstract
The study sought to investigate the potentials of axenic cultures of Pleurotus ostreatus, Phanerochaete chrysosporium and their coculture (P. chrysosporium and P. ostreatus) to break down lignin and to enhance the rumen fermentability of rice straw. Rice straw was fermented by two lignin-degrading fungi, namely, P. ostreatus, P. chrysosporium and its coculture (P. ostreatus and P. chrysosporium) with uninoculated straw as control under solid-state fermentation employing a completely randomized research design. The coculture exhibited a mutual intermingling plus inhibition interaction. The fungi treatment increased the crude protein from (5.1%) in the control to (6.5%, 6.6%, and 6.7%) in the P. ostreatus, P. chrysosporium and coculture respectively. The coculture treated straw had a lower lignin content (5.3%) compared to the P. chrysosporium (6.2%) with the P. ostreatus recording the least (3.3%) lignin fraction. Treatment of rice straw with coculture improved the in vitro dry matter digestibility (68.1%), total volatile fatty acids (35.3 mM), and total gas (57.4 ml/200 mg) compared to P. chrysosporium (45.1%, 32.2 mM, 44.4 ml/200 mg) but was second to P. ostreatus (75.3%, 38.3 mM, 65.6 ml/200 mg). Instead of an anticipated synergistic effect from the coculture, a competitive antagonistic effect was rather observed at the end of the study, a condition that can be attributed to the coculture behavior.
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9
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Schilling M, Maia-Grondard A, Baltenweck R, Robert E, Hugueney P, Bertsch C, Farine S, Gelhaye E. Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches. FRONTIERS IN PLANT SCIENCE 2022; 13:988709. [PMID: 36226293 PMCID: PMC9549746 DOI: 10.3389/fpls.2022.988709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/16/2022] [Indexed: 05/13/2023]
Abstract
Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called "amadou," one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites (extractives) and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species, and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche. Proteomics data are available via ProteomeXchange with identifier PXD036889.
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Affiliation(s)
- Marion Schilling
- Université de Lorraine, INRAE, IAM, Nancy, France
- *Correspondence: Marion Schilling,
| | | | | | | | | | - Christophe Bertsch
- Laboratoire Vigne Biotechnologies et Environnement UPR-3991, Université de Haute Alsace, Colmar, France
| | - Sibylle Farine
- Laboratoire Vigne Biotechnologies et Environnement UPR-3991, Université de Haute Alsace, Colmar, France
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, Nancy, France
- Eric Gelhaye,
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10
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Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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Mäki M, Mali T, Hellén H, Heinonsalo J, Lundell T, Bäck J. Deadwood substrate and species-species interactions determine the release of volatile organic compounds by wood-decaying fungi. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Baptista P, Guedes de Pinho P, Moreira N, Malheiro R, Reis F, Padrão J, Tavares R, Lino-Neto T. In vitro interactions between the ectomycorrhizal Pisolithus tinctorius and the saprotroph Hypholoma fasciculare fungi: morphological aspects and volatile production. Mycology 2021; 12:216-229. [PMID: 34552812 PMCID: PMC8451600 DOI: 10.1080/21501203.2021.1876778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ectomycorrhizal fungi are crucial for forests sustainability. For Castanea sativa, ectomycorrhizal fungus Pisolithus tinctorius is an important mutualist partner. Saprotrophic fungi Hypholoma fasciculare, although used for biocontrol of Armillaria root disease, it negatively affected the interaction between the P. tinctorius and plant host roots, by compromise the formation of P. tinctorius-C. sativa mycorrhizae. In this work, fungal morphology during inhibition of H. fasciculare against P. tinctorius was elucidated. P. tinctorius growth was strongly affected by H. fasciculare, which was significantly reduced after six days of co-culture and become even more significant through time. During this period, P. tinctorius developed vesicles and calcium oxalate crystals, which were described as mechanisms to stress adaption by fungi. H. fasciculare produced different volatile organic compounds in co-cultures over time and differ between single or in dual-species. H. fasciculare highly produced sesquiterpenes (namely, α-muurolene) and nitrogen-containing compounds, which are recognised as having antimicrobial activity.
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Affiliation(s)
- Paula Baptista
- Centro De Investigação De Montanha (CIMO), Instituto Politécnico De Bragança, Campus De Santa Apolónia, Bragança, Portugal
| | - Paula Guedes de Pinho
- UCIBIO-REQUIMTE/Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Nathalie Moreira
- UCIBIO-REQUIMTE/Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ricardo Malheiro
- Centro De Investigação De Montanha (CIMO), Instituto Politécnico De Bragança, Campus De Santa Apolónia, Bragança, Portugal
| | - Francisca Reis
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Jorge Padrão
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Rui Tavares
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
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13
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Decay stages of wood and associated fungal communities characterise diversity-decomposition relationships. Sci Rep 2021; 11:8972. [PMID: 33903719 PMCID: PMC8076174 DOI: 10.1038/s41598-021-88580-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/05/2021] [Indexed: 11/26/2022] Open
Abstract
The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.
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Smith GR, Peay KG. Multiple distinct, scale-dependent links between fungi and decomposition. Ecol Lett 2021; 24:1352-1362. [PMID: 33894029 DOI: 10.1111/ele.13749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 01/04/2023]
Abstract
Decomposition has historically been considered a function of climate and substrate but new research highlights the significant role of specific micro-organisms and their interactions. In particular, wood decay is better predicted by variation in fungal communities than in climate. Multiple links exist: interspecific competition slows decomposition in more diverse fungal communities, whereas trait variation between different communities also affects process rates. Here, we paired field and laboratory experiments using a dispersal gradient at a forest-shrubland ecotone to examine how fungi affect wood decomposition across scales. We observed that while fungal communities closer to forests were capable of faster decomposition, wood containing diverse fungal communities decomposed more slowly, independent of location. Dispersal-driven stochasticity in small-scale community assembly was nested within large-scale turnover in the regional species pool, decoupling the two patterns. We thus find multiple distinct links between microbes and ecosystem function that manifest across different spatial scales.
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Affiliation(s)
- Gabriel Reuben Smith
- Department of Biology, Stanford University, Stanford, CA, USA.,Global Ecosystem Ecology, Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
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15
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O'Leary J, Journeaux KL, Houthuijs K, Engel J, Sommer U, Viant MR, Eastwood DC, Müller C, Boddy L. Space and patchiness affects diversity-function relationships in fungal decay communities. THE ISME JOURNAL 2021; 15:720-731. [PMID: 33067587 PMCID: PMC8027639 DOI: 10.1038/s41396-020-00808-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 01/30/2023]
Abstract
The space in which organisms live determines health and physicality, shaping the way in which they interact with their peers. Space, therefore, is critically important for species diversity and the function performed by individuals within mixed communities. The biotic and abiotic factors defined by the space that organisms occupy are ecologically significant and the difficulty in quantifying space-defined parameters within complex systems limits the study of ecological processes. Here, we overcome this problem using a tractable system whereby spatial heterogeneity in interacting fungal wood decay communities demonstrates that scale and patchiness of territory directly influence coexistence dynamics. Spatial arrangement in 2- and 3-dimensions resulted in measurable metabolic differences that provide evidence of a clear biological response to changing landscape architecture. This is of vital importance to microbial systems in all ecosystems globally, as our results demonstrate that community function is driven by the effects of spatial dynamics.
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Affiliation(s)
- Jade O'Leary
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Katie L Journeaux
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Kas Houthuijs
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Jasper Engel
- NERC Biomolecular Analysis Facility-Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulf Sommer
- NERC Biomolecular Analysis Facility-Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mark R Viant
- NERC Biomolecular Analysis Facility-Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Carsten Müller
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
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16
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Fukasawa Y, Kaga K. Effects of wood resource size and decomposition on hyphal outgrowth of a cord-forming basidiomycete, Phanerochaete velutina. Sci Rep 2020; 10:21936. [PMID: 33318597 PMCID: PMC7736840 DOI: 10.1038/s41598-020-79058-8] [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: 08/19/2020] [Accepted: 12/03/2020] [Indexed: 11/09/2022] Open
Abstract
To assess the relationship between resource use and hyphal growth in a cord-forming basidiomycete, Phanerochaete velutina, soil microcosm experiments were conducted using wood blocks of three different sizes in three different soil quantities, thereby simulating the different amounts of available nutrients. The highest percentage weight loss was observed in the smallest wood blocks after a 27-d incubation period in soil microcosms, although the percentage weight loss over the 2-month pure culture colonization prior to inoculation was not significantly different among various block sizes. The greatest hyphal outgrowth was also observed in the smallest wood blocks and was positively associated with wood decay. The slopes of the regression lines between hyphal coverage and percentage wood mass loss were identical among different wood sizes, but the slopes between hyphal coverage and absolute wood mass loss were steeper in the smaller wood blocks than that in largest one. These results suggest that the level of intensity of mycelial foraging for new resources in the soil depends on the percentage of the amount of wood resource utilized, and not on the absolute amount of carbon obtained from the wood.
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Affiliation(s)
- Yu Fukasawa
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko, Osaki, Miyagi, 989-6711, Japan.
| | - Koji Kaga
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko, Osaki, Miyagi, 989-6711, Japan
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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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18
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Presley GN, Zhang J, Purvine SO, Schilling JS. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. Front Microbiol 2020; 11:1646. [PMID: 32849338 PMCID: PMC7399148 DOI: 10.3389/fmicb.2020.01646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023] Open
Abstract
Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
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Affiliation(s)
- Gerald N Presley
- Department of Wood Science and Engineering, Oregon State University, Corvallis, OR, United States
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
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Marini-Macouzet C, Muñoz L, Gonzalez-Rubio A, Eguiarte LE, Souza V, Velez P. Experimental Analysis of Interactions Among Saprotrophic Fungi from A Phosphorous-Poor Desert Oasis in the Chihuahuan Desert. MYCOBIOLOGY 2020; 48:410-417. [PMID: 33177920 PMCID: PMC7580559 DOI: 10.1080/12298093.2020.1788271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/22/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (Aspergillus niger, Cladosporium sp., and Coprinellus micaceus) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored in vitro under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in Cladosporium sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (Aeromonas spp. and Vibrio sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.
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Affiliation(s)
- Constanza Marini-Macouzet
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Muñoz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Aldo Gonzalez-Rubio
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Patricia Velez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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20
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Skelton J, Loyd A, Smith JA, Blanchette RA, Held BW, Hulcr J. Fungal symbionts of bark and ambrosia beetles can suppress decomposition of pine sapwood by competing with wood-decay fungi. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Fukasawa Y, Gilmartin EC, Savoury M, Boddy L. Inoculum volume effects on competitive outcome and wood decay rate of brown- and white-rot basidiomycetes. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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23
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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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24
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25
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Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils. Sci Rep 2018; 8:7866. [PMID: 29777126 PMCID: PMC5959846 DOI: 10.1038/s41598-018-25877-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon (14C) dating CO2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41–56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350–400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ13C values of CO2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa.
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26
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Singh D, Lee CH. Volatiles Mediated Interactions Between Aspergillus oryzae Strains Modulate Morphological Transition and Exometabolomes. Front Microbiol 2018; 9:628. [PMID: 29670599 PMCID: PMC5893800 DOI: 10.3389/fmicb.2018.00628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Notwithstanding its mitosporic nature, an improbable morpho-transformation state i. e., sclerotial development (SD), is vaguely known in Aspergillus oryzae. Nevertheless an intriguing phenomenon governing mold's development and stress response, the effects of exogenous factors engendering SD, especially the volatile organic compounds (VOCs) mediated interactions (VMI) pervasive in microbial niches have largely remained unexplored. Herein, we examined the effects of intra-species VMI on SD in A. oryzae RIB 40, followed by comprehensive analyses of associated growth rates, pH alterations, biochemical phenotypes, and exometabolomes. We cultivated A. oryzae RIB 40 (S1VMI: KACC 44967) opposite a non-SD partner strain, A. oryzae (S2: KCCM 60345), conditioning VMI in a specially designed “twin plate assembly.” Notably, SD in S1VMI was delayed relative to its non-conditioned control (S1) cultivated without partner strain (S2) in twin plate. Selectively evaluating A. oryzae RIB 40 (S1VMI vs. S1) for altered phenotypes concomitant to SD, we observed a marked disparity for corresponding growth rates (S1VMI < S1)7days, media pH (S1VMI > S1)7days, and biochemical characteristics viz., protease (S1VMI > S1)7days, amylase (S1VMI > nS1)3–7days, and antioxidants (S1VMI > S1)7days levels. The partial least squares—discriminant analysis (PLS-DA) of gas chromatography—time of flight—mass spectrometry (GC-TOF-MS) datasets for primary metabolites exhibited a clustered pattern (PLS1, 22.04%; PLS2, 11.36%), with 7 days incubated S1VMI extracts showed higher abundance of amino acids, sugars, and sugar alcohols with lower organic acids and fatty acids levels, relative to S1. Intriguingly, the higher amino acid and sugar alcohol levels were positively correlated with antioxidant activity, likely impeding SD in S1VMI. Further, the PLS-DA (PLS1, 18.11%; PLS2, 15.02%) based on liquid chromatography—mass spectrometry (LC-MS) datasets exhibited a notable disparity for post-SD (9–11 days) sample extracts with higher oxylipins and 13-desoxypaxilline levels in S1VMI relative to S1, intertwining Aspergillus morphogenesis and secondary metabolism. The analysis of VOCs for the 7 days incubated samples displayed considerably higher accumulation of C-8 compounds in the headspace of twin-plate experimental sets (S1VMI:S2) compared to those in non-conditioned controls (S1 and S2—without respective partner strains), potentially triggering altered morpho-transformation and concurring biochemical as well as metabolic states in molds.
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Affiliation(s)
- Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Choong H Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
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27
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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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28
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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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29
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Ujor VC, Adukwu EC, Okonkwo CC. Fungal wars: The underlying molecular repertoires of combating mycelia. Fungal Biol 2018; 122:191-202. [PMID: 29551193 DOI: 10.1016/j.funbio.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 10/18/2022]
Abstract
Non-self contact between fungi elicits strong morphological and biochemical reactions in the mycelia of interacting species. Although these reactions appear to be species- and interaction-specific, some responses such as pigmentation, increased secretion of phenol-oxidases, barrage formation and sealing of the mycelia front are common responses in most interactions. Hence, some species recruit similar molecular machineries in response to non-self. Increasing number of fully sequenced and annotated fungal genomes and advances in genome-wide and global proteome analytical tools now allow researchers to use techniques such as RNA sequencing, micro and macroarray analysis, 2-dimensional protein gel profiling, and differential display of mRNA to probe the underlying molecular mechanisms of combative mycelial interactions. This review provides an overview of the genes and proteins found to be differentially expressed in conflicting fungal mycelia by the use of 'omics' tools. Connections between observed gene and protein repertoires of competing mycelia and the attendant morphological and biochemical changes are presented.
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Affiliation(s)
- Victor C Ujor
- Bioenergy and Biological Waste Management Program, Agricultural Technical Institute, The Ohio State University, 1328 Dover Road, Wooster, OH, USA.
| | - Emmanuel C Adukwu
- Department of Applied Sciences, University of the West of England, Frenchay Campus, Cold Harbour Lane, Bristol, BS16 1QY, United Kingdom
| | - Christopher C Okonkwo
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Avenue, Wooster, OH, 44691, USA
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30
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Interactions between abundant fungal species influence the fungal community assemblage on limestone. PLoS One 2017; 12:e0188443. [PMID: 29211748 PMCID: PMC5718416 DOI: 10.1371/journal.pone.0188443] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/07/2017] [Indexed: 11/19/2022] Open
Abstract
The assembly of fungal communities on stone materials is mainly influenced by the differential bioreceptivity of such materials and environmental conditions. However, little is known about the role of fungal interactions in the colonization and establishment of fungal species. We analyzed the effects of intra- and interspecific interactions between 11 species of fungi in oligotrophic and copiotrophic media and on limestone coupons. In a previous study, these species were the most frequently isolated in the epilithic biofilms of limestone walls exposed to a subtropical climate. In the culture media, we found a greater frequency of intra- and interspecific inhibitory effects in the oligotrophic medium than in the copiotrophic medium. On the limestone coupons, all fungi were able to establish; however, the colonization success rate varied significantly. Cladosporium cladosporioides had a less extensive colonization in isolation (control) than in dual interactions (coexistence) with other species. Phoma eupyrena exhibited the highest colonization success rate and competitive dominance among all tested species. X-ray diffraction (XRD) and scanning electron microscope (SEM) analyses revealed that Pestalotiopsis maculans and Paraconiothyrium sp. produced calcium oxalate crystals during their growth on coupon surfaces, both in isolation and in dual interactions. Our results demonstrate that interactions between abundant fungal species influence the fungal colonization on substrates, the biomineralization and the fungal community assemblage growing in limestone biofilms.
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31
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Cline LC, Schilling JS, Menke J, Groenhof E, Kennedy PG. Ecological and functional effects of fungal endophytes on wood decomposition. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lauren C. Cline
- Department of Plant and Microbial BiologyUniversity of Minnesota St. Paul MN USA
| | - Jonathan S. Schilling
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
| | - Jon Menke
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
- Cargill Hopkins MN USA
| | - Emily Groenhof
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
| | - Peter G. Kennedy
- Department of Plant and Microbial BiologyUniversity of Minnesota St. Paul MN USA
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota St. Paul MN USA
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33
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Maynard DS, Crowther TW, Bradford MA. Fungal interactions reduce carbon use efficiency. Ecol Lett 2017; 20:1034-1042. [DOI: 10.1111/ele.12801] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/13/2017] [Accepted: 05/30/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Daniel S. Maynard
- School of Forestry and Environmental Studies Yale University 370 Prospect St New Haven CT USA
- Department of Ecology & Evolution University of Chicago 1101 E 57th Street Chicago IL60637 USA
| | - Thomas W. Crowther
- School of Forestry and Environmental Studies Yale University 370 Prospect St New Haven CT USA
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6708 PB The Netherlands
| | - Mark A. Bradford
- School of Forestry and Environmental Studies Yale University 370 Prospect St New Haven CT USA
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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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Hiscox J, Savoury M, Toledo S, Kingscott-Edmunds J, Bettridge A, Waili NA, Boddy L. Threesomes destabilise certain relationships: multispecies interactions between wood decay fungi in natural resources. FEMS Microbiol Ecol 2017; 93:2975568. [PMID: 28175239 PMCID: PMC5399798 DOI: 10.1093/femsec/fix014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/06/2017] [Indexed: 12/04/2022] Open
Abstract
Understanding interspecific interactions is key to explaining and modelling community development and associated ecosystem function. Most interactions research has focused on pairwise combinations, overlooking the complexity of multispecies communities. This study investigated three-way interactions between saprotrophic fungi in wood and across soil, and indicated that pairwise combinations are often inaccurate predictors of the outcomes of multispecies competition in wood block interactions. This inconsistency was especially true of intransitive combinations, resulting in increased species coexistence within the resource. Furthermore, the addition of a third competitor frequently destabilised the otherwise consistent outcomes of pairwise combinations in wood blocks, which occasionally resulted in altered resource decomposition rates, depending on the relative decay abilities of the species involved. Conversely, interaction outcomes in soil microcosms were unaffected by the presence of a third combatant. Multispecies interactions promoted species diversity within natural resources, and made community dynamics less consistent than could be predicted from pairwise interaction studies.
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Affiliation(s)
- Jennifer Hiscox
- Corresponding author: School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK. Tel. +442920 875384; E-mail:
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Buchkowski RW, Bradford MA, Grandy AS, Schmitz OJ, Wieder WR. Applying population and community ecology theory to advance understanding of belowground biogeochemistry. Ecol Lett 2017; 20:231-245. [DOI: 10.1111/ele.12712] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/27/2016] [Accepted: 11/13/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Robert W. Buchkowski
- School of Forestry & Environmental Studies Yale University New Haven CT06511 USA
| | - Mark A. Bradford
- School of Forestry & Environmental Studies Yale University New Haven CT06511 USA
| | - Andrew Stuart Grandy
- Department of Natural Resources and the Environment University of New Hampshire Durham NH03824 USA
| | - Oswald J. Schmitz
- School of Forestry & Environmental Studies Yale University New Haven CT06511 USA
| | - William R. Wieder
- Climate and Global Dynamics Laboratory National Center for Atmospheric Research Boulder CO80307 USA
- Institute of Arctic and Alpine Research University of Colorado Boulder CO80309 USA
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Li W, Wang M, Bian X, Guo J, Cai L. A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition. Front Microbiol 2016; 7:2098. [PMID: 28066402 PMCID: PMC5179519 DOI: 10.3389/fmicb.2016.02098] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
The intertidal region is one of the most dynamic environments in the biosphere, which potentially supports vast biodiversity. Fungi have been found to play important roles in marine ecosystems, e.g., as parasites or symbionts of plants and animals, and as decomposers of organic materials. The fungal diversity in intertidal region, however, remains poorly understood. In this study, sediment samples from various intertidal habitats of Chinese seas were collected and investigated for determination of fungal community and spatial distribution. Through ribosomal RNA internal transcribed spacer-2 (ITS2) metabarcoding, a high-level fungal diversity was revealed, as represented by 6,013 OTUs that spanned six phyla, 23 classes, 84 orders and 526 genera. The presence of typical decomposers (e.g., Corollospora in Ascomycota and Lepiota in Basidiomycota) and pathogens (e.g., Olpidium in Chytriomycota, Actinomucor in Zygomycota and unidentified Rozellomycota spp.), and even mycorrhizal fungi (e.g., Glomus in Glomeromycota) indicated a complicated origin of intertidal fungi. Interestingly, a small proportion of sequences were classified to obligate marine fungi (e.g., Corollospora, Lignincola, Remispora, Sigmoidea). Our data also showed that the East China Sea significantly differed from other regions in terms of species richness and community composition, indicating a profound effect of the huge discharge of the Yangtze River. No significant difference in fungal communities was detected, however, among habitat types (i.e., aquaculture, dock, plant, river mouth and tourism). These observations raise further questions on adaptation of these members to environments and the ecological functions they probably perform.
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Affiliation(s)
- Wei Li
- College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Mengmeng Wang
- College of Marine Life Sciences, Ocean University of ChinaQingdao, China; State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences (CAS), BeijingChina
| | - Xiaomeng Bian
- College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Jiajia Guo
- College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing China
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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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Hiscox J, Savoury M, Johnston SR, Parfitt D, Müller CT, Rogers HJ, Boddy L. Location, location, location: priority effects in wood decay communities may vary between sites. Environ Microbiol 2016; 18:1954-69. [PMID: 26626102 DOI: 10.1111/1462-2920.13141] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Priority effects are known to have a major influence on fungal community development in decomposing wood, but it has not yet been established whether these effects are consistent between different geographical locations. Here, beech (Fagus sylvatica) wood disks that had been pre-colonized with three wood decay basidiomycetes were placed in seven woodland sites with similar characteristics for 12-24 months, and the successor communities profiled using culture-based techniques coupled with amplicon sequencing. On the majority of sites, assembly history differed as a result of primary versus secondary resource capture only (i.e. different communities developed in uncolonized control disks compared with those that had been pre-colonized), but on certain sites distinct successor communities followed each pre-colonizer species. This study provides preliminary evidence that differences in abiotic factors and species pools between sites can cause spatial variation in how priority effects influence wood decay communities.
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Affiliation(s)
- Jennifer Hiscox
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Melanie Savoury
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Sarah R Johnston
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - David Parfitt
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
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Jomura M, Akashi Y, Itoh H, Yuki R, Sakai Y, Maruyama Y. Biotic and Abiotic Factors Controlling Respiration Rates of Above- and Belowground Woody Debris of Fagus crenata and Quercus crispula in Japan. PLoS One 2015; 10:e0145113. [PMID: 26658727 PMCID: PMC4682764 DOI: 10.1371/journal.pone.0145113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 11/28/2015] [Indexed: 11/18/2022] Open
Abstract
As a large, long-term pool and source of carbon and nutrients, woody litter is an important component of forest ecosystems. The objective of this study was to estimate the effect of the factors that regulate the rate of decomposition of coarse and fine woody debris (CFWD) of dominant tree species in a cool-temperate forest in Japan. Respiration rates of dead stems, branches, and coarse and fine roots of Fagus crenata and Quercus crispula felled 4 years prior obtained in situ ranged from 20.9 to 500.1 mg CO2 [kg dry wood]–1 h–1 in a one-time measurement in summer. Respiration rate had a significant negative relationship with diameter; in particular, that of a sample of Q. crispula with a diameter of >15 cm and substantial heartwood was low. It also had a significant positive relationship with moisture content. The explanatory variables diameter, [N], wood density, and moisture content were interrelated. The most parsimonious path model showed 14 significant correlations among 8 factors and respiration. Diameter and [C] had large negative direct effects on CFWD respiration rate, and moisture content and species had medium positive direct effects. [N] and temperature did not have direct or indirect effects, and position and wood density had indirect effects. The model revealed some interrelationships between controlling factors. We discussed the influence of the direct effects of explanatory variables and the influence especially of species and position. We speculate that the small R2 value of the most parsimonious model was probably due to the omission of microbial biomass and activity. These direct and indirect effects and interrelationships between explanatory variables could be used to develop a process-based CFWD decomposition model.
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Affiliation(s)
- Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
- * E-mail:
| | - Yuhei Akashi
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Hiromu Itoh
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Risa Yuki
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Yoshimi Sakai
- Kyusyu Research Center, Forestry and Forest Products Research Institute, Kumamoto, Kumamoto, Japan
| | - Yutaka Maruyama
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
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Oliver JP, Schilling JS. Applying trait-function relationships for microbial plant decomposition to predict medium longevity in pollution control biofilters. Appl Microbiol Biotechnol 2015; 100:2843-53. [PMID: 26590583 DOI: 10.1007/s00253-015-7134-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/25/2015] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
Abstract
Biofilters, bioreactors used for pollution control, can effectively treat a variety of odorous and hazardous emissions, but uncertain medium longevities and associated costs limit biofilter adoption. To improve medium-life estimations for biofilter end-users, litter bags were used to compare decay rates of common biofilter medium types and test the effects of nitrogen (N) enrichment and livestock production emissions on medium decay in a full-scale biofilter over a 27-month period. Generally, "by-product" media (mulch, corn cobs) decayed faster than hardwood media, with decay of softwood media the slowest. Analysis showed nutrient content was the best predictor of early-stage decay, while carbon fractions and nutrient content best predicted medium longevity. N amendments and N-rich barn emissions were found to hasten medium decay. By identifying decay rates and rate predictors specific for biofilter media, we provide biofilter engineers and farmers with a quantitative way to improve medium selection based on the trade-offs between medium cost and replacement frequency.
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Affiliation(s)
- Jason P Oliver
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Kaufert Laboratory, 2004 Folwell Ave., St. Paul, MN, 55108, USA
| | - Jonathan S Schilling
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Kaufert Laboratory, 2004 Folwell Ave., St. Paul, MN, 55108, USA. .,Institute on the Environment, University of Minnesota, 325 LES Building, 1954 Buford Ave, St. Paul, MN, 55108, USA.
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Hiscox J, Savoury M, Müller CT, Lindahl BD, Rogers HJ, Boddy L. Priority effects during fungal community establishment in beech wood. THE ISME JOURNAL 2015; 9:2246-60. [PMID: 25798754 PMCID: PMC4579477 DOI: 10.1038/ismej.2015.38] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/28/2015] [Accepted: 02/06/2015] [Indexed: 11/13/2022]
Abstract
Assembly history of fungal communities has a crucial role in the decomposition of woody resources, and hence nutrient cycling and ecosystem function. However, it has not been clearly determined whether the fungal species that arrive first may, potentially, dictate the subsequent pathway of community development, that is, whether there is a priority effect at the species level. We used traditional culture-based techniques coupled with sequencing of amplified genetic markers to profile the fungal communities in beech (Fagus sylvatica) disks that had been pre-colonised separately with nine species from various stages of fungal succession. Clear differences in community composition were evident following pre-colonisation by different species with three distinct successor communities identified, indicating that individual species may have pivotal effects in driving assembly history. Priority effects may be linked to biochemical alteration of the resource and combative ability of the predecessor.
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Affiliation(s)
- Jennifer Hiscox
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Melanie Savoury
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
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45
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Blumenstein K, Macaya-Sanz D, Martín JA, Albrectsen BR, Witzell J. Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes. Front Microbiol 2015; 6:1033. [PMID: 26441951 PMCID: PMC4585013 DOI: 10.3389/fmicb.2015.01033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/11/2015] [Indexed: 12/31/2022] Open
Abstract
There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.
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Affiliation(s)
- Kathrin Blumenstein
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, AlnarpSweden
| | - David Macaya-Sanz
- Department of Natural Systems and Resources, School of Forest Engineers, Technical University of MadridMadrid, Spain
| | - Juan A. Martín
- Department of Natural Systems and Resources, School of Forest Engineers, Technical University of MadridMadrid, Spain
| | - Benedicte R. Albrectsen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå UniversityUmeå, Sweden
- Department of Plant and Environmental Sciences, University of CopenhagenCopenhagen, Denmark
| | - Johanna Witzell
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, AlnarpSweden
- School of Forest Sciences, Faculty of Science and Forestry, University of Eastern Finland, JoensuuFinland
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