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Purahong W, Ji L, Wu YT. Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing. MICROBIAL ECOLOGY 2024; 87:66. [PMID: 38700528 PMCID: PMC11068674 DOI: 10.1007/s00248-024-02372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
- School of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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Buba T, Ezra AG, Bako SP, Sabo MU. Seed germination dynamics of some woody legumes: implication for restoration of arid zones ecosystems. BIOTECHNOLOGIA 2023; 104:381-402. [PMID: 38213475 PMCID: PMC10777726 DOI: 10.5114/bta.2023.132774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/19/2023] [Accepted: 08/17/2023] [Indexed: 01/13/2024] Open
Abstract
The seed germination dynamics of Acacia nilotica, Bauhinia rufescens, Faidherbia albida, and Piliostigma reticulatum were investigated over 28 days. Seeds were pretreated with concentrated sulfuric acid. Determined germination parameters included germination energy, germination period, germination capacity, germination inertia, and viability loss. Seeds exposed to sulfuric acid for extended periods (30, 40, 50, and 60 min) exhibited a higher germination rate (α = 0.05). For A. nilotica seeds, the 50 min acid treatment resulted in the highest germination energy of 85.5% and germination capacity of 89.5% (P = 0.001); conversely, the 60-min treatment yielded the highest germination energy and capacity, both 96.5% (P = 0.079), for P. reticulatum. In the case of B. rufescens, the 30-min treatment led to the highest germination energy of 93% and germination capacity of 88% (P = 0.001). For F. albida, all acid treatments resulted in 100% for both germination energy and germination capacity (P = 0.621). Viability losses for A. nilotica and P. reticulatum were higher (32 and 30%, respectively) than those for B. rufescens and F. albida, which were 19.5 and 6%, respectively (P = 0.000). Generally, higher germination energy resulted in lower viability loss, dependent on the species. Analyses of germination inertia and viability loss suggest that seeds of A. nilotica and P. reticulatum possess a greater ability to survive in arid land climates than those of B. rufescens and F. albida. However, due to the advantage of lower viability loss, B. rufescens and F. albida should be preferred for the natural restoration of arid land ecosystems where seed availability is a major concern.
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Affiliation(s)
- Toma Buba
- Department of Biological Sciences, Faculty of Science, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Abalis Gaya Ezra
- Department of Biological Sciences, Faculty of Science, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Sunday Paul Bako
- Department of Biological Science, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Mohammad Umar Sabo
- Department of Crop Production, Faculty Agriculture, Abubakar Tafawa Balewa University, Bauchi, Nigeria
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3
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Buffi M, Cailleau G, Kuhn T, Li Richter XY, Stanley CE, Wick LY, Chain PS, Bindschedler S, Junier P. Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. MICROLIFE 2023; 4:uqad042. [PMID: 37965130 PMCID: PMC10642649 DOI: 10.1093/femsml/uqad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.
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Affiliation(s)
- Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, P.O. Box 1663, NM 87545, United States
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Liu H, Wang S, Lang B, Li Y, Wang X, Chen J. Fused expression of Sm1-Chit42 proteins for synergistic mycoparasitic response of Trichoderma afroharzianum on Botrytis cinerea. Microb Cell Fact 2023; 22:156. [PMID: 37592265 PMCID: PMC10433591 DOI: 10.1186/s12934-023-02151-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
Sm1 and Chit42 of Trichoderma have been universally confirmed as crucial biocontrol factors against pathogen infection through induced resistance and mycoparasitism, respectively. However, not enough work has been conducted to understand the novel function of fused expression of these two proteins in Trichoderma. The results of this study demonstrated that Sm1-Chit42 protein (SCf) engineered T. afroharzianum strain OE:SCf exerted synergistic inhibition to Botrytis cinerea growth at multiple stages of mycoparasitic interaction of T. afroharzianum and B. cinerea including chemotropism sensing, hyphal coiling, hydrophobicity modulation, cell wall adhesion, virulence reduction and pathogen killing by ROS. These results highlight a novel mycoparasitic system in Trichoderma strains engineered with Sm1-Chit42 chimeric protein to combat B. cinerea growth and reproduction, which would lay a strong foundation for exploring a new engineered Trichoderma biofungicide created with chimeric proteins in the future.
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Affiliation(s)
- Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoqing Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Lang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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5
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Substrate affinities of wood decay fungi are foremost structured by wood properties not climate. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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6
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Tanunchai B, Ji L, Schröder O, Gawol SJ, Geissler A, Wahdan SFM, Buscot F, Kalkhof S, Schulze ED, Noll M, Purahong W. Fate of a biodegradable plastic in forest soil: Dominant tree species and forest types drive changes in microbial community assembly, influence the composition of plastisphere, and affect poly(butylene succinate-co-adipate) degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162230. [PMID: 36796697 DOI: 10.1016/j.scitotenv.2023.162230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Poly(butylene succinate-co-adipate) (PBSA) degradation and its plastisphere microbiome in cropland soils have been studied; however, such knowledge is limited in the case of forest ecosystems. In this context, we investigated: i) the impact of forest types (conifer and broadleaved forests) on the plastisphere microbiome and its community assembly, ii) their link to PBSA degradation, and iii) the identities of potential microbial keystone taxa. We determined that forest type significantly affected microbial richness (F = 5.26-9.88, P = 0.034 to 0.006) and fungal community composition (R2 = 0.38, P = 0.001) of the plastisphere microbiome, whereas its effects on microbial abundance and bacterial community composition were not significant. The bacterial community was governed by stochastic processes (mainly homogenizing dispersal), whereas the fungal community was driven by both stochastic and deterministic processes (drift and homogeneous selection). The highest molar mass loss was found for PBSA degraded under Pinus sylvestris (26.6 ± 2.6 to 33.9 ± 1.8 % (mean ± SE) at 200 and 400 days, respectively), and the lowest molar mass loss was found under Picea abies (12.0 ± 1.6 to 16.0 ± 0.5 % (mean ± SE) at 200 and 400 days, respectively). Important fungal PBSA decomposers (Tetracladium) and atmospheric dinitrogen (N2)-fixing bacteria (symbiotic: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Methylobacterium and non-symbiotic: Mycobacterium) were identified as potential keystone taxa. The present study is among the first to determine the plastisphere microbiome and its community assembly processes associated with PBSA in forest ecosystems. We detected consistent biological patterns in the forest and cropland ecosystems, indicating a potential mechanistic interaction between N2-fixing bacteria and Tetracladium during PBSA biodegradation.
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Affiliation(s)
- Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Li Ji
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; School of Forestry, Central South of Forestry and Technology, 410004 Changsha, PR China
| | - Olaf Schröder
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Susanne Julia Gawol
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Andreas Geissler
- Department of Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Darmstadt D-64287, Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; Department of Botany and Microbiology, Faculty of Science, Suez Canal University, 41522 Ismailia, Egypt
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Stefan Kalkhof
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany.
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany.
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Garcia-Lopez MT, Serrano MS, Camiletti BX, Gordon A, Estudillo C, Trapero A, Diez CM, Moral J. Study of the competition between Colletotrichum godetiae and C. nymphaeae, two pathogenic species in olive. Sci Rep 2023; 13:5344. [PMID: 37005485 PMCID: PMC10067957 DOI: 10.1038/s41598-023-32585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Olive anthracnose, a critical olive fruit disease that adversely impacts oil quality, is caused by Colletotrichum species. A dominant Colletotrichum species and several secondary species have been identified in each olive-growing region. This study surveys the interspecific competition between C. godetiae, dominant in Spain, and C. nymphaeae, prevalent in Portugal, to shed light on the cause of this disparity. When Petri-dishes of Potato Dextrose Agar (PDA) and diluted PDA were co-inoculated with spore mixes produced by both species, C. godetiae displaced C. nymphaeae, even if the percentage of spores in the initial spore mix inoculation was just 5 and 95%, respectively. The C. godetiae and C. nymphaeae species showed similar fruit virulence in separate inoculations in both cultivars, the Portuguese cv. Galega Vulgar and the Spanish cv. Hojiblanca, and no cultivar specialization was observed. However, when olive fruits were co-inoculated, the C. godetiae species showed a higher competitive ability and partially displaced the C. nymphaeae species. Furthermore, both Colletotrichum species showed a similar leaf survival rate. Lastly, C. godetiae was more resistant to metallic copper than C. nymphaeae. The work developed here allows a deeper understanding of the competition between C. godetiae and C. nymphaeae, which could lead to developing strategies for more efficient disease risk assessment.
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Affiliation(s)
- M Teresa Garcia-Lopez
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
- Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - M Socorro Serrano
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Boris X Camiletti
- Department of Plant Pathology, University of California-Davis, Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - Ana Gordon
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Cristina Estudillo
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Antonio Trapero
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Concepcion M Diez
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain
| | - Juan Moral
- Department of Agronomy, Maria de Maeztu Excellence Unit, University of Cordoba, Edif. C4, Campus de Rabanales, 14071, Cordoba, Spain.
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Lee J, Yun J, Yang Y, Jung JY, Lee YK, Yuan J, Ding W, Freeman C, Kang H. Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2647-2659. [PMID: 36719133 DOI: 10.1021/acs.est.2c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, BangorLL57 2UW, U.K
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
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10
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Probst M, Telagathoti A, Siewert B, Khomenko I, Betta E, Biasioli F, Peintner U. Co-cultivation of Mortierellaceae with Pseudomonas helmanticensis affects both their growth and volatilome. Sci Rep 2023; 13:2213. [PMID: 36750680 PMCID: PMC9905594 DOI: 10.1038/s41598-023-29134-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Volatile organic compounds (VOCs) might mediate microbial interactions, especially in spatially structured environments, such as soil. However, the variety and specificity of VOC production are poorly understood. Here, we studied 25 Mortierellaceae strains belonging to the genera Linnemannia and Entomortierella in both pure and co-culture with Pseudomonas helmanticensis under laboratory conditions. We analysed both the fungal growth depending on co-cultivation and the cultures' volatilomes applying proton-transfer-reaction time-of-flight and gas chromatography-mass spectrometry (PTR-ToF-MS and GC-MS). In a strain-specific manner, we found the fungi's radial growth rate and colony morphology affected by the presence of P. helmanticensis. The fungus seemed to generally reduce the bacterial growth. The volatilomes of the fungal and bacterial pure and co-cultures were diverse. While the fungi frequently consumed VOCs, P. helmanticensis produced a higher diversity and amount of VOCs than any fungal strain. Our results support that both the pure and co-culture volatilomes are taxonomically conserved. Taken together, our data supports the relevance of VOCs in Mortierellaceae-P. helmanticensis interaction. We also discuss individual VOCs that appear relevant in the interaction.
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Affiliation(s)
- Maraike Probst
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Anusha Telagathoti
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Bianka Siewert
- Institute of Pharmacy, Center for Chemistry and Biomedicine, Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Innrain 80 - 82/IV, 6020, Innsbruck, Austria
| | - Iuliia Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Emanuela Betta
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Ursula Peintner
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Valette N, Legout A, Goodell B, Alfredsen G, Auer L, Gelhaye E, Derrien D. Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Lee J, Zhou X, Seo YO, Lee ST, Yun J, Yang Y, Kim J, Kang H. Effects of vegetation shift from needleleaf to broadleaf species on forest soil CO 2 emission. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158907. [PMID: 36150592 DOI: 10.1016/j.scitotenv.2022.158907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Forest soil harbors diverse microbial communities with decisive roles in ecosystem processes. Vegetation shift from needleleaf to broadleaf species is occurring across the globe due to climate change and anthropogenic activities, potentially change forest soil microbial communities and C cycle. However, our knowledge on the impact of such vegetation shift on soil microbial community and activities, and its consequences on forest soil C dynamics are still not well established. Here, we examined the seasonal variation of soil CO2 emission, soil extracellular enzyme activities (EEAs), and soil bacterial, fungal communities in subtropical forest from broadleaf, needleleaf, and mixed stands. In addition, soil CO2 emission and soil EEAs were measured in temperate forest during the growing season. Soil organic matter (SOM) content significantly differs between broadleaf and needleleaf forests and primarily distinguish various soil chemical and microbial characteristics. Significantly higher EEAs and soil CO2 emission in broadleaf forest compared to needleleaf forest were observed both in subtropical and temperate forests. The relative abundance of Basidiomycota positively correlated with SOM and EEAs and indirectly increase soil CO2 emission whereas the relative abundance of Ascomycota exhibits opposite trend, suggesting that soil fungal communities play a key role in determining the different microbial activities between broadleaf and needleleaf stands. The temperature sensitivity of soil CO2 emission was significantly higher in broadleaf forest compared to needleleaf forest, further suggesting that the soil organic carbon in broadleaf forests is more vulnerable to warming.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; College of Agricultural Science and Engineering, Hohai University, China
| | - Yeon Ok Seo
- Warm Temperate and Subtropical Forest Research Center, National Institute of Forest Science, Republic of Korea
| | - Sang Tae Lee
- Lab of Silvicultural Practices and Management, National Institute of Forest Science, Republic of Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea.
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13
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Cook K, Taylor AD, Sharma J, Taylor DL. Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02104-7. [PMID: 36048179 DOI: 10.1007/s00248-022-02104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.
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Affiliation(s)
- Kel Cook
- Department of Biology, University of New Mexico, Castetter Hall 1480, MSC03-2020, 219 Yale Blvd NE, Albuquerque, NM, 87131-0001, USA.
| | - Andrew D Taylor
- Department of Biology, University of Hawai'i at Manoa, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI, 96822, USA
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Bayer Plant Science Building, Room 219, 2911 15th Street, Mail Stop 2122, Lubbock, TX, 79409-2122, USA
| | - D Lee Taylor
- Department of Biology, University of New Mexico, Castetter Hall 1480, MSC03-2020, 219 Yale Blvd NE, Albuquerque, NM, 87131-0001, USA
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14
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Duong HL, Paufler S, Harms H, Schlosser D, Maskow T. Fungal Lignocellulose Utilisation Strategies from a Bioenergetic Perspective: Quantification of Related Functional Traits Using Biocalorimetry. Microorganisms 2022; 10:microorganisms10081675. [PMID: 36014092 PMCID: PMC9415514 DOI: 10.3390/microorganisms10081675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, and zygomycete species, were investigated in a standardised laboratory environment, employing wheat straw as a globally relevant lignocellulosic substrate. Our study demonstrates that biocalorimetry can be employed successfully to determine growth-related fungal activity parameters, such as apparent maximum growth rates (AMGR), cultivation times until the observable onset of fungal growth at AMGR (tAMGR), quotients formed from the AMGR and tAMGR (herein referred to as competitive growth potential, CGP), and heat yield coefficients (YQ/X), the latter indicating the degree of resource investment into fungal biomass versus other functional attributes. These parameters seem suitable to link fungal potentials for biomass production to corresponding ecological strategies employed during resource utilisation, and therefore may be considered as fungal life history traits. A close connection exists between the CGP and YQ/X values, which suggests an interpretation that relates to fungal life history strategies.
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Affiliation(s)
- Hieu Linh Duong
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Faculty of Engineering, Vietnamese-German University (VGU), Le Lai Street, Hoa Phu Ward, Thủ Dầu Một 7500, Binh Duong, Vietnam
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
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15
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Antifungal Activity of Datura stramonium L. Extractives against Xylophagous Fungi. FORESTS 2022. [DOI: 10.3390/f13081222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Some plants have great resistance against herbivores, invertebrates, insects, bacteria, and fungi. This resistance is mostly present in plants containing alkaloids, which are the substances responsible for giving them defensive properties. The genus Datura contains tropane alkaloids and all plants from this genus have defensive properties. In this work, we report the toxic effect against fungi of Datura stramonium extracts, obtained by the Petri dish method. The extraction solvents were water, ethanol, 2-propanol, n-butanol, propanone, butanone, 3-methyl-2-pentanone, dichloromethane, xylene, and toluene. The test fungi were Trametes versicolor (L. ex. Fr) Pilát and Rhodonia placenta (Fr.) Niemelä, K.H.Larss. & Schigel. It was found that water, butanone, and toluene extracts promoted mycelial growth, xylene extracts neither inhibited nor promoted mycelial growth, while the other extracts slightly inhibited the growth of these fungi.
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16
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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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17
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Pasailiuk MV, Sukhomlyn MM, Fontana NM. Influence of rutin on fruiting of Hericium coralloides, Polyporus umbellatus, and Flammulina velutipes. Mycologia 2022; 114:1-9. [PMID: 35584030 DOI: 10.1080/00275514.2022.2051972] [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: 02/26/2021] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
We studied the effect of rutin on mycelial growth and fruiting of Hericium coralloides, Polyporus umbellatus, and Flammulina velutipes on sunflower husks and on agar nutrient media. On sunflower husks, rutin (300 mg/30 g husk) inhibits the mycelial growth of H. coralloides, but the formation of fruiting bodies of the fungus occurs 3 weeks earlier than on the substrate, where rutin was not used. In half of the cases with rutin, we observed two waves of fungus fruiting. The weight of fruiting bodies formed on sunflower husks with rutin was 2.5 times greater than the weight of fruiting bodies formed on sunflower husks without rutin. For P. umbellatus and F. velutipes, adding rutin (300 mg/30 g husk) confers no net benefit. On wort agar (WA), the addition of rutin at concentrations of 50, 100, 200, and 300 mg per Petri dish inhibits the mycelial growth of H. coralloides but stimulates the rapid emergence of the fungus fruiting bodies rudiments. For F. velutipes on WA, rutin accelerates the complete overgrowth of the fungus on the Petri dish twice as fast, but it is not effective for accelerating fruiting. Rutin does not stimulate the formation sclerotia of P. umbellatus. Due to the fact that rutin is a stimulant of fruiting bodies only for H. coralloides, we believe that the initiating mechanism causing fungal fruiting is not isolated only to rutin. However, it may be more widely effective in influencing growth in mycelium than is shown in this study due to a limited number of strains. Production of metabolites as a result of secondary synthesis need to be tested as do more strains/species from a diverse group of Agaricomycetes.
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Affiliation(s)
| | - Maryna M Sukhomlyn
- Department of Population Dynamics, Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine, Kyiv, UA-03143, Ukraine
| | - Nina M Fontana
- Department of Native American Studies, University of California, Davis, California 95616
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18
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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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19
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Toapanta-Alban CE, Ordoñez ME, Blanchette RA. New Findings on the Biology and Ecology of the Ecuadorian Amazon Fungus Polyporus leprieurii var. yasuniensis. J Fungi (Basel) 2022; 8:jof8020203. [PMID: 35205957 PMCID: PMC8874993 DOI: 10.3390/jof8020203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
Polyporus leprieurii var. yasuniensis is a prolific wood-decay fungus inhabiting the forest floor of one of the most biodiverse places on earth, the Yasuní National Park in Ecuador. Basidiocarps and aerial rhizomorphs are commonly found growing on woody debris distributed along the floor of this forest ecosystem. Because of the extraordinary abundance of this fungus in the tropical rainforest, we carried out investigations to better understand the biological and ecological aspects contributing to its prolific distribution. Data on growth inhibition in paired competition studies with sixteen fungal isolates exemplifies defense mechanisms used to defend its territory, including pseudosclerotial plates and the development of a melanized rhizomorphic mat. Results of biomass loss on eleven types of tropical wood in microcosm experiments demonstrated the broad decay capacity of the fungus. In and ex situ observations provided information on how long rhizomorphs can prevail in highly competitive ecosystems as well as stressful conditions in the laboratory. Finally, high concentrations of metal ions occur on rhizomorphs as compared to colonized wood. Sequestration of metal ions from the environment by the melanized rhizomorphs may offer protection against competitors. The development of melanized rhizomorphs is key to find and colonize new substrates and resist changing environmental conditions.
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Affiliation(s)
| | - María E. Ordoñez
- Fungarium QCAM, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador;
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA;
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20
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Dou K, Pang G, Cai F, Chenthamara K, Zhang J, Liu H, Druzhinina IS, Chen J. Functional Genetics of Trichoderma Mycoparasitism. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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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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22
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Abrego N. Wood-inhabiting fungal communities: Opportunities for integration of empirical and theoretical community ecology. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Aleklett K, Boddy L. Fungal behaviour: a new frontier in behavioural ecology. Trends Ecol Evol 2021; 36:787-796. [PMID: 34172318 DOI: 10.1016/j.tree.2021.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022]
Abstract
As human beings, behaviours make up our everyday lives. What we do from the moment we wake up to the moment we go back to sleep at night can all be classified and studied through the concepts of behavioural ecology. The same applies to all vertebrates and, to some extent, invertebrates. Fungi are, in most people's eyes perhaps, the eukaryotic multicellular organisms with which we humans share the least commonalities. However, they still express behaviours, and we argue that we could obtain a better understanding of their lives - although they are very different from ours - through the lens of behavioural ecology. Moreover, insights from fungal behaviour may drive a better understanding of behavioural ecology in general.
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Affiliation(s)
- Kristin Aleklett
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, SE-234 22 Lomma, Sweden.
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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24
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Sperandio GB, Filho EXF. An overview of Trichoderma reesei co-cultures for the production of lignocellulolytic enzymes. Appl Microbiol Biotechnol 2021; 105:3019-3025. [PMID: 33825000 DOI: 10.1007/s00253-021-11261-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 12/01/2022]
Abstract
Biorefineries are core facilities for implementing a sustainable circular bioeconomy. These facilities rely on microbial enzymes to hydrolyze lignocellulosic substrates into fermentable sugars. Fungal co-cultures mimic the process of natural biodegradation and have been shown to increase certain enzyme activities. Trichoderma reesei and its many mutant strains are major cellulase producers and are heavily utilized as a source of carbohydrate-active enzymes. Several reports have demonstrated that T. reesei co-cultures present higher enzyme activities compared with its monocultures, especially in the context of β-glucosidase activity. The performance of T. reesei during co-culturing has been assessed with several fungal partners, including Aspergillus niger, one of the most recurrent partners. Various aspects of co-cultivation still need further investigation, especially regarding the molecular interactions between fungi in controlled environments and the optimization of the resulting enzyme cocktails. Since plenty of genetic and physiological data on T. reesei is available, the species is an outstanding candidate for future co-culture investigations. Co-cultures are still a developing field for industrial enzyme production, and many aspects of the technique need further improvement before real applications. KEY POINTS: • T. reesei co-cultures are an alternative for producing lignocellulolytic enzymes. • Several reports suggest an increase in certain enzyme activities in co-cultures. • More in-depth investigations of co-cultures are necessary for advancing this field.
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25
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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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26
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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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27
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Biocatalytic potential of basidiomycetes: Relevance, challenges and research interventions in industrial processes. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Wang P, Zhang G, Wei XY, Liu R, Gu JJ, Cao FF. Bioselective Synthesis of a Porous Carbon Collector for High-Performance Sodium-Metal Anodes. J Am Chem Soc 2021; 143:3280-3283. [PMID: 33645987 DOI: 10.1021/jacs.0c12098] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomass-derived carbon materials prepared via pyrolysis from natural wood structures show potential for a storage application. Natural wood is composed of multiple carbon sources, including lignin, hemicellulose, and cellulose, which influence the formation and microstructure of pyrolysis carbon. However, the mechanism is not fully understood. In this work, vast lignin is selectively consumed via biodegradation with fungi from basswood. The results demonstrate that the as-prepared carbon material has a short-range ordered graphitic structure after thermal treatment. The improved graphitization degree of carbon suggests that cellulose is beneficial to graphite formation during pyrolysis. The elevated graphitization degree helps to improve the charge transfer and the thermodynamic stability of the electrode reaction. As a proof of concept, the obtained carbon current collector as a sodium-metal anode can undergo cycling at an areal capacity of 10 mAh cm-2 for over 4500 h and yield an excellent Coulombic efficiency of >99.5%.
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Affiliation(s)
- Ping Wang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Geng Zhang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xu-Yang Wei
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Rui Liu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jiang-Jiang Gu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Fei-Fei Cao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, P. R. China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, P. R. China
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Whiteford R, Nurika I, Schiller T, Barker G. The white-rot fungus, Phanerochaete chrysosporium, under combinatorial stress produces variable oil profiles following analysis of secondary metabolites. J Appl Microbiol 2021; 131:1305-1317. [PMID: 33484615 DOI: 10.1111/jam.15013] [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: 06/29/2020] [Revised: 11/10/2020] [Accepted: 01/15/2021] [Indexed: 11/29/2022]
Abstract
AIMS The effects of combinatorial stress on lipid production in Phanerochaete chrysosporium remain understudied. This species of white-rot fungi was cultivated on solid-state media while under variable levels of known abiotic and biotic stressors to establish the effect upon fungal oil profiles. METHODS AND RESULTS Environmental stressors induced upon the fungus included the following: temperature, nutrient limitation and interspecies competition to assess impact upon oil profiles. Fatty acid type and its concentration were determined using analytical methods of gas chromatography and mass spectrometry. Growth rate under stress was established using high-performance liquid chromatography with ergosterol as the biomarker. Fungi grown on solid-state agar were able to simultaneously produce short- and long-chain fatty acids which appeared to be influenced by nutritional composition as well as temperature. Addition of nitrogen supplements increased the growth rate, but lipid dynamics remained unchanged. Introducing competition-induced stress had significantly altered the production of certain fatty acids beyond that of the monoculture while under nutrient-limiting conditions. Linoleic acid concentrations, for example, increased from an average of 885 ng μl-1 at monoculture towards 13 820 ng μl-1 at co-culture, following 7 days of incubation. CONCLUSIONS Interspecies competition produced the most notable impact on lipid production for solid-state media cultivated fungi while the addition of nitrogen supplementation presented growth and lipid accumulation to be uncorrelated. Combinatorial stress therefore influences the yield of overall lipid production as well as the number of intermediate fatty acids produced, deriving similar oil profiles to the composition of vegetable and fish oils. SIGNIFICANCE AND IMPACT OF THE STUDY Fungal secondary metabolism remains highly sensitive following combinatorial stress. The outcome impacts the research towards optimizing fungal oil profiles for biomass and nutrition. Future investigations on fungal stress tolerance mechanisms need to address these environmental factors throughout the experimental design.
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Affiliation(s)
- R Whiteford
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - I Nurika
- Department of Agroindustrial Technology, Faculty of Agricultural Technology, University of Brawijaya, Malang, Indonesia
| | - T Schiller
- Warwick Manufacturing Group, The University of Warwick, Coventry, UK
| | - G Barker
- School of Life Sciences, The University of Warwick, Coventry, UK
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Wesener F, Szymczak A, Rillig MC, Tietjen B. Stress priming affects fungal competition - evidence from a combined experimental and modelling study. Environ Microbiol 2021; 23:5934-5945. [PMID: 33538387 DOI: 10.1111/1462-2920.15418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 12/01/2022]
Abstract
Priming, an inducible stress defence strategy that prepares an organism for an impending stress event, is common in microbes and has been studied mostly in isolated organisms or populations. How the benefits of priming change in the microbial community context and, vice versa, whether priming influences competition between organisms, remain largely unknown. In this study, we grew different isolates of soil fungi that experienced heat stress in isolation and pairwise competition experiments and assessed colony extension rate as a measure of fitness under priming and non-priming conditions. Based on this data, we developed a cellular automaton model simulating the growth of the ascomycete Chaetomium angustispirale competing against other fungi and systematically varied fungal response traits to explain similarities and differences observed in the experimental data. We showed that competition changes the priming benefit compared with isolated growth and that it can even be reversed depending on the competitor's traits such as growth rate, primeability and stress susceptibility. With this study, we transfer insights on priming from studies in isolation to competition between species. This is an important step towards understanding the role of inducible defences in microbial community assembly and composition.
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Affiliation(s)
- Felix Wesener
- Institute of Biology, Theoretical Ecology, Freie Universität Berlin, Königin-Luise-Str. 2/4, Gartenhaus, Berlin, 14195, Germany
| | - Aleksandra Szymczak
- Institute of Biology, Ecology of Plants, Freie Universität Berlin, Altensteinstraße 6, Berlin, 14195, Germany
| | - Matthias C Rillig
- Institute of Biology, Ecology of Plants, Freie Universität Berlin, Altensteinstraße 6, Berlin, 14195, Germany.,Berlin Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Britta Tietjen
- Institute of Biology, Theoretical Ecology, Freie Universität Berlin, Königin-Luise-Str. 2/4, Gartenhaus, Berlin, 14195, Germany.,Berlin Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
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31
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Wu D, Pietsch KA, Staab M, Yu M. Wood species identity alters dominant factors driving fine wood decomposition along a tree diversity gradient in subtropical plantation forests. Biotropica 2021. [DOI: 10.1111/btp.12906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donghao Wu
- College of Life Sciences Zhejiang University Hangzhou China
| | - Katherina A. Pietsch
- Institute of Systematic Botany and Functional Biodiversity University of Leipzig Leipzig Germany
| | - Michael Staab
- Department of Nature Conservation and Landscape Ecology Albert‐Ludwigs‐University Freiburg Freiburg Germany
| | - Mingjian Yu
- College of Life Sciences Zhejiang University Hangzhou China
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Nicault M, Zaiter A, Dumarcay S, Chaimbault P, Gelhaye E, Leblond P, Bontemps C. Elicitation of Antimicrobial Active Compounds by Streptomyces-Fungus Co-Cultures. Microorganisms 2021; 9:microorganisms9010178. [PMID: 33467607 PMCID: PMC7830452 DOI: 10.3390/microorganisms9010178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
The bacteria of the genus Streptomyces and Basidiomycete fungi harbor many biosynthetic gene clusters (BGCs) that are at the origin of many bioactive molecules with medical or industrial interests. Nevertheless, most BGCs do not express in standard lab growth conditions, preventing the full metabolic potential of these organisms from being exploited. Because it generates biotic cues encountered during natural growth conditions, co-culture is a means to elicit such cryptic compounds. In this study, we explored 72 different Streptomyces-fungus interaction zones (SFIZs) generated during the co-culture of eight Streptomyces and nine fungi. Two SFIZs were selected because they showed an elicitation of anti-bacterial activity compared to mono-cultures. The study of these SFIZs showed that co-culture had a strong impact on the metabolic expression of each partner and enabled the expression of specific compounds. These results show that mimicking the biotic interactions present in this ecological niche is a promising avenue of research to explore the metabolic capacities of Streptomyces and fungi.
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Affiliation(s)
- Matthieu Nicault
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France;
| | - Ali Zaiter
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France; (A.Z.); (P.C.)
| | | | | | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France;
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Correspondence: (P.L.); (C.B.)
| | - Cyril Bontemps
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France;
- Correspondence: (P.L.); (C.B.)
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Abstract
Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils. IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.
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Invasion of an inconspicuous ambrosia beetle and fungus may affect wood decay in Southeastern North America. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02448-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Croitoru C, Roata IC. Ionic Liquids as Antifungal Agents for Wood Preservation. Molecules 2020; 25:E4289. [PMID: 32962068 PMCID: PMC7570619 DOI: 10.3390/molecules25184289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Ionic liquids represent a class of highly versatile organic compounds used extensively in the last decade for lignocellulose biomass fractionation and dissolution, as well as property modifiers for wood materials. This review is dedicated to the use of ionic liquids as antifungal agents for wood preservation. Wood preservation against fungal attack represents a relatively new domain of application for ionic liquids, emerging in the late 1990s. Comparing to other application domains of ionic liquids, this particular one has been relatively little researched. Ionic liquids may be promising as wood preservatives due to their ability to swell wood, which translates into better penetration ability and fixation into the bulk of the wood material than other conventional antifungal agents, avoiding leaching over time. The antifungal character of ionic liquids depends on the nature of their alkyl-substituted cation, on the size and position of their substituents, and of their anion. It pertains to a large variety of wood-colonizing fungi, both Basidiomycetes and Fungiimperfecti.
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Affiliation(s)
- Catalin Croitoru
- Materials Engineering and Welding Department, Transilvania University of Brasov, Eroilor 29 Blvd., 500039 Brasov, Romania
| | - Ionut Claudiu Roata
- Materials Engineering and Welding Department, Transilvania University of Brasov, Eroilor 29 Blvd., 500039 Brasov, Romania
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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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Chen G, Yu H, Lin F, Zhang Z, Yan B, Song Y. Utilization of edible fungi residues towards synthesis of high-performance porous carbon for effective sorption of Cl-VOCs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138475. [PMID: 32334213 DOI: 10.1016/j.scitotenv.2020.138475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/12/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Edible fungi residues are natural fungi etching feedstock that provide loose structure with multidimensional framework. These advantages help KOH to penetrate rigid cytoderm into innermost space and attain porous carbon with high porosity. Utilization of edible fungi residue not only avoids artificial operation of fungal inoculation and culture steps, but also provides new method for waste disposal. As expected, carbon derived from three fungi residues attains excellent porosity. The highest surface area reaches 3463.3 m2/g, which is approximately 2 and 6 times higher than original biomass (1630.7 m2/g) and commercial carbon (691.1 m2/g), respectively. Filiform structures derived from hyphae growth contribute to pores formation. Coprinus comatus fungi residue as optimal raw material obtains hierarchical pore channel with dominant micropores (76%) and natural nitrogen doping (1.28 at.%). The highest DCM and CB adsorption capacities attain 716.9 and 641.7 mg/g, respectively, which are 13 and 6 times higher than that of commercial carbon. The positive effects from fungi growth improve DCM adsorption particularly. DCM adsorption over fungi residues derived carbon is twice higher than original biomass carbon. Competitive adsorption, recyclability, surface variations and desorption components after saturated adsorption are fully investigated for practical application. The present study provides a new insight for developing high-value technology for synthesizing Cl-VOCs adsorbents using edible fungi residues.
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Affiliation(s)
- Guanyi Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China
| | - Hongdi Yu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China
| | - Fawei Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China.
| | - Zhiman Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China
| | - Beibei Yan
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China
| | - Yingjin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China; Tianjin Key Lab of Biomass/Wastes Utilization, Tianjin University, Tianjin 300072, PR China
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38
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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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The Evolutionary and Functional Paradox of Cerato-platanins in Fungi. Appl Environ Microbiol 2020; 86:AEM.00696-20. [PMID: 32332135 DOI: 10.1128/aem.00696-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 01/11/2023] Open
Abstract
Cerato-platanins (CPs) form a family of fungal small secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis of 283 CPs from 157 fungal genomes with the focus on the environmental opportunistic plant-beneficial and mycoparasitic fungus Trichoderma Our results revealed a long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of Trichoderma, while some species have up to four CP-encoding genes. All Trichoderma CPs evolve under stabilizing natural selection pressure. The functional genomic analysis of CPs in Trichoderma guizhouense and Trichoderma harzianum revealed that only epl1 is active at all stages of development but that it plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by Trichoderma spp. Similarly, biochemical tests of EPL1 heterologously produced by Pichia pastoris support the claims described above. Based on the results obtained, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelia and, thus, facilitate the nutritional versatility of fungi. The effector-like functions do not sufficiently describe the diversity and evolution of these proteins in fungi, as they are also maintained, duplicated, or laterally transferred in the genomes of nonherbivore fungi.IMPORTANCE Cerato-platanins (CPs) are surface-active small proteins abundantly secreted by filamentous fungi. Consequently, immune systems of plants and other organisms recognize CPs and activate defense mechanisms. Some CPs are toxic to plants and act as virulence factors in plant-pathogenic fungi. Our analysis, however, demonstrates that the interactions with plants do not explain the origin and evolution of CPs in the fungal kingdom. We revealed a long evolutionary history of CPs with multiple cases of gene duplication and events of interfungal lateral gene transfers. In the mycoparasitic Trichoderma spp., CPs evolve under stabilizing natural selection and hamper the colonization of roots. We propose that the ability to modify the hydrophobicity of the fungal hyphosphere is a key to unlock the evolutionary and functional paradox of these proteins.
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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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Abstract
As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.
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Medina EQ, Oliveira AS, Medina HR, Rangel DE. Serendipity in the wrestle between Trichoderma and Metarhizium. Fungal Biol 2020; 124:418-426. [DOI: 10.1016/j.funbio.2020.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/21/2019] [Accepted: 01/02/2020] [Indexed: 01/06/2023]
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Wen Z, Zeng Z, Ren F, Asiegbu FO. The Conifer Root and Stem Rot Pathogen ( Heterobasidion parviporum): Effectome Analysis and Roles in Interspecific Fungal Interactions. Microorganisms 2019; 7:microorganisms7120658. [PMID: 31817407 PMCID: PMC6955712 DOI: 10.3390/microorganisms7120658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion parviporum Niemelä & Korhonen is an economically important basidiomycete, causing root and stem rot disease of Norway spruce (Picea abies (L.) Karst) in Northern Europe. The H. parviporum genome encodes numerous small secreted proteins, which might be of importance for interacting with mycorrhiza symbionts, endophytes, and other saprotrophs. We hypothesized that small secreted proteins from H. parviporum (HpSSPs) are involved in interspecific fungal interaction. To identify HpSSP-coding genes potentially involved, we screened the H. parviporum effectome and compared their transcriptomic profiles during fungal development and in planta tree infection. We further conducted phylogenetic analysis, and identified a subset of hypothetical proteins with nonpredicted domain or unknown function as HpSSPs candidates for further characterization. The HpSSPs candidates were selected based on high-quality sequence, cysteine residue frequency, protein size, and in planta expression. We subsequently explored their roles during in vitro interaction in paired cultures of H. parviporum with ectomycorrhizal Cortinarius gentilis, endophytic Phialocephala sphaeroides, saprotrophs (Mycena sp., Phlebiopsis gigantea, and Phanerochaete chrysosporium), respectively. The transcriptomic profile revealed that a large proportion of effector candidates was either barely expressed or highly expressed under all growth conditions. In vitro dual-culture test showed that P. sphaeroides and C. gentilis were overgrown by H. parviporum. The barrage zone formation or no physical contact observed in paired cultures with the saprotrophs suggest they had either combative interaction or antibiosis effect with H. parviporum. Several HpSSPs individuals were up- or downregulated during the nonself interactions. The results of HpSSPs gene expression patterns provide additional insights into the diverse roles of SSPs in tree infection and interspecific fungal interactions.
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Affiliation(s)
- Zilan Wen
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
| | - Fei Ren
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, No. 1 Shuiza Road, Beijing 102300, China
| | - Fred O. Asiegbu
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
- Correspondence: ; Tel.: +358-294158109
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Genetic and Functional Diversity of Nitrilases in Agaricomycotina. Int J Mol Sci 2019; 20:ijms20235990. [PMID: 31795104 PMCID: PMC6928751 DOI: 10.3390/ijms20235990] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/27/2022] Open
Abstract
Nitrilases participate in the nitrile metabolism in microbes and plants. They are widely used to produce carboxylic acids from nitriles. Nitrilases were described in bacteria, Ascomycota and plants. However, they remain unexplored in Basidiomycota. Yet more than 200 putative nitrilases are found in this division via GenBank. The majority of them occur in the subdivision Agaricomycotina. In this work, we analyzed their sequences and classified them into phylogenetic clades. Members of clade 1 (61 proteins) and 2 (25 proteins) are similar to plant nitrilases and nitrilases from Ascomycota, respectively, with sequence identities of around 50%. The searches also identified five putative cyanide hydratases (CynHs). Representatives of clade 1 and 2 (NitTv1 from Trametes versicolor and NitAg from Armillaria gallica, respectively) and a putative CynH (NitSh from Stereum hirsutum) were overproduced in Escherichia coli. The substrates of NitTv1 were fumaronitrile, 3-phenylpropionitrile, β-cyano-l-alanine and 4-cyanopyridine, and those of NitSh were hydrogen cyanide (HCN), 2-cyanopyridine, fumaronitrile and benzonitrile. NitAg only exhibited activities for HCN and fumaronitrile. The substrate specificities of these nitrilases were largely in accordance with substrate docking in their homology models. The phylogenetic distribution of each type of nitrilase was determined for the first time.
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Norberg A, Halme P, Kotiaho JS, Toivanen T, Ovaskainen O. Experimentally induced community assembly of polypores reveals the importance of both environmental filtering and assembly history. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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Castro VRD, de Castro Freitas MP, Zanuncio AJV, Zanuncio JC, Surdi PG, Carneiro ADCO, Vital BR. Resistance of in natura and torrefied wood chips to xylophage fungi. Sci Rep 2019; 9:11068. [PMID: 31363114 PMCID: PMC6667691 DOI: 10.1038/s41598-019-47398-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/16/2019] [Indexed: 01/09/2023] Open
Abstract
The diversity of fungi allows for their colonisation in different environments, including wood destined for power generation, with an ability to degrade or hinder its use. Torrefaction or pre-carbonisation, a low oxygenation heat treatment with temperatures between 200 and 300 °C, accumulates carbon and lignin, decreases hygroscopicity, increases energy efficiency and reduces the wood attractiveness to xylophagous microorganisms. This work aimed to study the resistance of Eucalyptus urophylla wood chips, submitted to torrefaction temperatures of 180, 220 and 260 °C for 20 minutes, to xylophagous fungi, according to the ASTM D-2017 method (2005). The white rot fungi Phanerochaete chrysosporium, Pleurotus ostreatus and Trametes versicolor and the brown rot fungus Gloeophyllum trabeum were used. After 12 weeks of exposure, the mass losses of wood samples in natura and torrified at 180 °C attacked by Pleurotus ostreatus and Trametes versicolor was higher. Torrefaction increased the resistance to fungi; the treatment at 260 °C was the most efficient with lower mass losses caused by fungi attacks and, consequently, greater resistance to the fungi tested.
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Affiliation(s)
| | | | | | - José Cola Zanuncio
- Departamento de Entomologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Paula Gabriella Surdi
- Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | | | - Benedito Rocha Vital
- Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
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O'Leary J, Hiscox J, Eastwood DC, Savoury M, Langley A, McDowell SW, Rogers HJ, Boddy L, Müller CT. The whiff of decay: Linking volatile production and extracellular enzymes to outcomes of fungal interactions at different temperatures. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Oberlies NH, Knowles SL, Amrine CSM, Kao D, Kertesz V, Raja HA. Droplet probe: coupling chromatography to the in situ evaluation of the chemistry of nature. Nat Prod Rep 2019; 36:944-959. [PMID: 31112181 DOI: 10.1039/c9np00019d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2019The chemistry of nature can be beautiful, inspiring, beneficial and poisonous, depending on perspective. Since the isolation of the first secondary metabolites roughly two centuries ago, much of the chemical research on natural products has been both reductionist and static. Typically, compounds were isolated and characterized from the extract of an entire organism from a single time point. While there could be subtexts to that approach, the general premise has been to determine the chemistry with very little in the way of tools to differentiate spatial and/or temporal changes in secondary metabolite profiles. However, the past decade has seen exponential advances in our ability to observe, measure, and visualize the chemistry of nature in situ. Many of those techniques have been reviewed in this journal, and most are tapping into the power of mass spectrometry to analyze a plethora of sample types. In nearly all of the other techniques used to study chemistry in situ, the element of chromatography has been eliminated, instead using various ionization sources to coax ions of the secondary metabolites directly into the mass spectrometer as a mixture. Much of that science has been driven by the great advances in ambient ionization techniques used with a suite of mass spectrometry platforms, including the alphabet soup from DESI to LAESI to MALDI. This review discusses the one in situ analysis technique that incorporates chromatography, being the droplet-liquid microjunction-surface sampling probe, which is more easily termed "droplet probe". In addition to comparing and contrasting the droplet probe with other techniques, we provide perspective on why scientists, particularly those steeped in natural products chemistry training, may want to include chromatography in in situ analyses. Moreover, we provide justification for droplet sampling, especially for samples with delicate and/or non-uniform topographies. Furthermore, while the droplet probe has been used the most in the analysis of fungal cultures, we digest a variety of other applications, ranging from cyanobacteria, to plant parts, and even delicate documents, such as herbarium specimens.
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Affiliation(s)
- Nicholas H Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Sonja L Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Chiraz Soumia M Amrine
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Diana Kao
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Vilmos Kertesz
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huzefa A Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
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Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environ Microbiol 2019; 21:2644-2658. [PMID: 30815928 PMCID: PMC6850483 DOI: 10.1111/1462-2920.14575] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/01/2022]
Abstract
When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin‐encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H2O2), which is stored in microscopic bag‐like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H2O2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H2O2 in signalling and fungal communication.
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Affiliation(s)
- Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Mohammad Javad Rahimi
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Hong Zhu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Andrei Steindorff
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sabine Schiessler
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Guan Pang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Yu Xu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Christian P Kubicek
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.,Steinschoetelgasse 7,1100, Vienna, Austria
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Irina S Druzhinina
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
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