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Dong W, Chen J, Liao X, Chen X, Huang L, Huang J, Huang R, Zhong S, Zhang X. Biodiversity, Distribution and Functional Differences of Fungi in Four Species of Corals from the South China Sea, Elucidated by High-Throughput Sequencing Technology. J Fungi (Basel) 2024; 10:452. [PMID: 39057337 PMCID: PMC11278478 DOI: 10.3390/jof10070452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Recent studies have predominantly spotlighted bacterial diversity within coral microbiomes, leaving coral-associated fungi in the shadows of scientific inquiry. This study endeavors to fill this knowledge gap by delving into the biodiversity, distribution and functional differences of fungi associated with soft corals Cladiella krempfi and Sarcophyton tortuosum, gorgonian coral Dichotella gemmacea and stony coral Favia speciosa from the South China Sea. Leveraging high-throughput sequencing of fungal internal transcribed spacer-1 (ITS1) region of the rRNA gene, a total of 431 fungal amplicon sequence variants (ASVs) were identified in this study, which indicated that a large number of fungal communities were harbored in the South China Sea corals. Noteworthy among our findings is that 10 fungal genera are reported for the first time in corals, with Candolleomyces, Exophiala, Fomitopsis, Inaequalispora, Kneiffiella, Paraphaeosphaeria, and Yamadazyma belonging to the Ascomycota, and Cystobasidium, Psathyrella, and Solicoccozyma to the Basidiomycota. Moreover, significant differences (p < 0.05) of fungal communities were observed among the various coral species. In particular, the gorgonian coral D. gemmacea emerged as a veritable haven for fungal diversity, boasting 307 unique ASVs. Contrastingly, soft corals S. tortuosum and C. krempfi exhibited modest fungal diversity, with 36 and 21 unique ASVs, respectively, while the stony coral F. speciosa hosted a comparatively sparse fungal community, with merely 10 unique ASVs in total. These findings not only provide basic data on fungal diversity and function in the South China Sea corals, but also underscore the imperative of nuanced conservation and management strategies for coral reef ecosystems worldwide.
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Affiliation(s)
- Wenyu Dong
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jiatao Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
| | - Xinyu Liao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
| | - Xinye Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
| | - Liyu Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
| | - Jiayu Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
| | - Riming Huang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510642, China;
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiaoyong Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (W.D.); (L.H.); (J.H.)
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Embacher J, Zeilinger S, Kirchmair M, Rodriguez-R LM, Neuhauser S. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Di Lella S, La Porta N, Tognetti R, Lombardi F, Nardin T, Larcher R. White rot fungal impact on the evolution of simple phenols during decay of silver fir wood by UHPLC-HQOMS. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:170-183. [PMID: 34322910 PMCID: PMC9290616 DOI: 10.1002/pca.3077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Silver fir (Abies alba Mill.) is one of the most valuable conifer wood species in Europe. Among the main opportunistic pathogens that cause root and butt rot on silver fir are Armillaria ostoyae and Heterobasidion abietinum. Due to the different enzymatic pools of these wood-decay fungi, different strategies in metabolizing the phenols were available. OBJECTIVE This work explores the changes in phenolic compounds during silver fir wood degradation. METHODOLOGY Phenols were analyzed before and after fungus inoculation in silver fir macerated wood after 2, 4 and 6 months. All samples were analyzed using high-performance liquid chromatography coupled to a hybrid quadrupole-orbitrap mass spectrometer. RESULTS Thirteen compounds, including simple phenols, alkylphenyl alcohols, hydroxybenzoketones, hydroxycinnamaldehydes, hydroxybenzaldehydes, hydroxyphenylacetic acids, hydroxycinnamic acids, hydroxybenzoic acids and hydroxycoumarins, were detected. Pyrocatechol, coniferyl alcohol, acetovanillone, vanillin, benzoic acid, 4-hydroxybenzoic acid and vanillic acid contents decreased during the degradation process. Methyl vanillate, ferulic acid and p-coumaric were initially produced and then degraded. Scopoletin was accumulated. Pyrocatechol, acetovanillone and methyl vanillate were found for the first time in both degrading and non-degrading wood of silver fir. CONCLUSIONS Despite differences in the enzymatic pool, both fungi caused a significant decrease in the amounts of phenolic compounds with the accumulation of the only scopoletin. Principal component analysis revealed an initial differentiation between the degradation activity of the two fungal species during degradation, but similar phenolic contents at the end of wood degradation.
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Affiliation(s)
- Stefania Di Lella
- Department of Biosciences and TerritoryUniversity of MolisePescheItaly
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
- Department of Agricultural, Environmental and Food SciencesUniversity of MoliseCampobassoItaly
| | - Nicola La Porta
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
- The EFI Project Centre on Mountain Forests (MOUNTFOR)Edmund Mach FoundationTrentoItaly
| | - Roberto Tognetti
- Department of Agricultural, Environmental and Food SciencesUniversity of MoliseCampobassoItaly
- The EFI Project Centre on Mountain Forests (MOUNTFOR)Edmund Mach FoundationTrentoItaly
| | - Fabio Lombardi
- Department of AgrariaUniversity Mediterranea of Reggio CalabriaReggio CalabriaItaly
| | - Tiziana Nardin
- Technology Transfer CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Roberto Larcher
- Technology Transfer CentreFondazione Edmund MachSan Michele all'AdigeItaly
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Lee M, Powell JR, Oberle B, Unda F, Mansfield SD, Dalrymple R, Rigg J, Cornwell WK, Zanne AE. Initial wood trait variation overwhelms endophyte community effects for explaining decay trajectories. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marissa Lee
- Department of Biological Sciences The George Washington University Washington DC United States
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment University of Western Sydney Hawkesbury Australia
| | - Brad Oberle
- Division of Natural Sciences New College of Florida Sarasota FL United States
| | - Faride Unda
- Department of Wood Science University of British Columbia Vancouver Canada
| | - Shawn D. Mansfield
- Department of Wood Science University of British Columbia Vancouver Canada
| | - Rhiannon Dalrymple
- Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences University of New South Wales Sydney Australia
| | - Jessica Rigg
- Elizabeth Macarthur Agricultural Institute Department of Primary Industries NSW Meanagle Australia
| | - William K. Cornwell
- Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences University of New South Wales Sydney Australia
| | - Amy E. Zanne
- Department of Biological Sciences The George Washington University Washington DC United States
- Department of Biology University of Miami Miami FL United States
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Successional Development of Fungal Communities Associated with Decomposing Deadwood in a Natural Mixed Temperate Forest. J Fungi (Basel) 2021; 7:jof7060412. [PMID: 34070657 PMCID: PMC8228407 DOI: 10.3390/jof7060412] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/29/2022] Open
Abstract
Deadwood represents an important carbon stock and contributes to climate change mitigation. Wood decomposition is mainly driven by fungal communities. Their composition is known to change during decomposition, but it is unclear how environmental factors such as wood chemistry affect these successional patterns through their effects on dominant fungal taxa. We analysed the deadwood of Fagus sylvatica and Abies alba across a deadwood succession series of >40 years in a natural fir-beech forest in the Czech Republic to describe the successional changes in fungal communities, fungal abundance and enzymatic activities and to link these changes to environmental variables. The fungal communities showed high levels of spatial variability and beta diversity. In young deadwood, fungal communities showed higher similarity among tree species, and fungi were generally less abundant, less diverse and less active than in older deadwood. pH and the carbon to nitrogen ratio (C/N) were the best predictors of the fungal community composition, and they affected the abundance of half of the dominant fungal taxa. The relative abundance of most of the dominant taxa tended to increase with increasing pH or C/N, possibly indicating that acidification and atmospheric N deposition may shift the community composition towards species that are currently less dominant.
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Vivelo S, Bhatnagar JM. An evolutionary signal to fungal succession during plant litter decay. FEMS Microbiol Ecol 2020; 95:5565043. [PMID: 31574146 PMCID: PMC6772037 DOI: 10.1093/femsec/fiz145] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Ecologists have frequently observed a pattern of fungal succession during litter decomposition, wherein different fungal taxa dominate different stages of decay in individual ecosystems. However, it is unclear which biological features of fungi give rise to this pattern. We tested a longstanding hypothesis that fungal succession depends on the evolutionary history of species, such that different fungal phyla prefer different decay stages. To test this hypothesis, we performed a meta-analysis across studies in 22 different ecosystem types to synthesize fungal decomposer abundances at early, middle and late stages of plant litter decay. Fungal phyla varied in relative abundance throughout decay, with fungi in the Ascomycota reaching highest relative abundance during early stages of decay (P < 0.001) and fungi in the Zygomycota reaching highest relative abundance during late stages of decay (P < 0.001). The best multiple regression model to explain variation in abundance of these fungal phyla during decay included decay stage, as well as plant litter type and climate factors. Most variation in decay-stage preference of fungal taxa was observed at basal taxonomic levels (phylum and class) rather than finer taxonomic levels (e.g. genus). For many finer-scale taxonomic groups and functional groups of fungi, plant litter type and climate factors were better correlates with relative abundance than decay stage per se, suggesting that the patchiness of fungal community composition in space is related to both resource and climate niches of different fungal taxa. Our study indicates that decomposer fungal succession is partially rooted in fungal decomposers’ deep evolutionary history, traceable to the divergence among phyla.
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Affiliation(s)
- Sasha Vivelo
- Dept. of Biology, Boston University, Boston, MA 02215, USA
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Aspects Determining the Dominance of Fomitopsis pinicola in the Colonization of Deadwood and the Role of the Pathogenicity Factor Oxalate. FORESTS 2020. [DOI: 10.3390/f11030290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbon and mineral cycling in sustainable forest systems depends on a microbiome of basidiomycetes, ascomycetes, litter-degrading saprobes, ectomycorrhizal, and mycoparasitic fungi that constitute a deadwood degrading consortium. The brown rot basidiomycete Fomitopsis pinicola (Swartz: Fr.) P. Karsten (Fp), as an oxalate-producing facultative pathogen, is an early colonizer of wounded trees and fresh deadwood. It replaces basidiomycetous white rot fungi and non-basidiomycetous fungal phyla in the presence of its volatilome, but poorly in its absence. With the goal of determining its dominance over the most competitive basidiomycetes and its role in fungal successions within the forest microbiome in general, Fp was exposed to the white rot fungus Kuehneromyces mutabilis (Schaeff.: Fr.) Singer & Smith (Km) in aseptic dual culture established on fertilized 100 mm-long wood dust columns in glass tubes with the inclusion of their volatilomes. For the mycelia approaching from the opposite ends of the wood dust columns, the energy-generating systems of laccase and manganese peroxidase (MnP), the virulence factor oxalate, and the exhalation of terpenes were determined by spectrophotometry, High Pressure Liquid Chromatography (HPLC), and Gas Chromatography-Mass Spectrometry (GC-MS). Km mycelia perceived the approaching Fp over 20 mm of non-colonized wood dust, reduced the laccase activity to 25%, and raised MnP to 275%–500% by gaining energy and presumably by controlling oxalate, H2O2, and the dropping substrate pH caused by Fp. On mycelial contact, Km stopped Fp, secured its substrate sector with 4 mm of an impermeable barrier region during an eruption of antimicrobial bisabolenes, and dropped from the invasion mode of substrate colonization into the steady state mode of low metabolic and defensive activity. The approaching Fp raised the oxalate production throughout to >20 g kg−1 to inactivate laccase and caused, with pH 1.4–1.7, lethal conditions in its substrate sector whose physiological effects on Km could be reproduced with acidity conditions incited by HCl. After a mean lag phase of 11 days, Fp persisting in a state of high metabolic activity overgrew and digested the debilitated Km thallus and terminated the production of oxalate. It is concluded that the factors contributing to the competitive advantage of F. pinicola in the colonization of wounded trees and pre-infected deadwood are the drastic long-term acidification of the timber substrate, its own insensitivity to extremely low pH conditions, its efficient control of the volatile mono- and sesquiterpenes of timber and microbial origin, and the action of a undefined blend of terpenes and allelopathic substances.
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Lee MR, Powell JR, Oberle B, Cornwell WK, Lyons M, Rigg JL, Zanne AE. Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats. Ecology 2019; 100:e02790. [PMID: 31228251 DOI: 10.1002/ecy.2790] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 04/14/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022]
Abstract
Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.
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Affiliation(s)
- Marissa R Lee
- Department of Biological Sciences, The George Washington University, Washington, D.C., 20052, USA
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Brad Oberle
- Division of Natural Sciences, New College of Florida, Sarasota, Florida, 34243, USA
| | - William K Cornwell
- School of Biological, Earth & Environmental Sciences, Ecology and Evolution Research Centre, UNSW Australia, Sydney, New South Wales, 2052, Australia
| | - Mitchell Lyons
- School of Biological, Earth & Environmental Sciences, Centre for Ecosystem Science, UNSW Australia, Sydney, New South Wales, 2052, Australia
| | - Jessica L Rigg
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Meanagle, New South Wales, 2568, Australia
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, Washington, D.C., 20052, USA
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Moose RA, Schigel D, Kirby LJ, Shumskaya M. Dead wood fungi in North America: an insight into research and conservation potential. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.32.30875] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Saproxylic fungi act as keystone species in forest ecosystems because they colonise and decompose dead wood, facilitating colonisation by later species. Here, we review the importance of intact forest ecosystems to dead wood fungi, as well as trends in their diversity research and challenges in conservation. Saproxylic communities are sensitive to transition from virgin forests to managed ecosystems, since the latter often results in reduced tree diversity and the removal of their natural habitat dead wood. The impact of dead wood management can be quite significant since many saproxylic fungi are host-specific. The significance of citizen science and educational programmes for saproxylic mycology is discussed with the emphasis on the North American region. We intend to raise the awareness of the role that dead wood fungi play in forest health in order to support development of corresponding conservational programmes.
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Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes. Appl Environ Microbiol 2018; 84:AEM.01133-18. [PMID: 30097442 DOI: 10.1128/aem.01133-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/04/2018] [Indexed: 11/20/2022] Open
Abstract
Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.
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Jacobsen RM, Sverdrup‐Thygeson A, Kauserud H, Mundra S, Birkemoe T. Exclusion of invertebrates influences saprotrophic fungal community and wood decay rate in an experimental field study. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13196] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rannveig M. Jacobsen
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
- The Norwegian Institute for Nature Research Oslo Norway
| | - Anne Sverdrup‐Thygeson
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Tone Birkemoe
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
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Birkemoe T, Jacobsen RM, Sverdrup-Thygeson A, Biedermann PHW. Insect-Fungus Interactions in Dead Wood Systems. SAPROXYLIC INSECTS 2018. [DOI: 10.1007/978-3-319-75937-1_12] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Mali T, Kuuskeri J, Shah F, Lundell TK. Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes. PLoS One 2017; 12:e0185171. [PMID: 28953947 PMCID: PMC5617175 DOI: 10.1371/journal.pone.0185171] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.
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Affiliation(s)
- Tuulia Mali
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Firoz Shah
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Taina Kristina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
- * E-mail:
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Chang C, Wu F, Yang W, Xu Z, Cao R, He W, Tan B, Justine MF. The microbial community in decaying fallen logs varies with critical period in an alpine forest. PLoS One 2017; 12:e0182576. [PMID: 28787465 PMCID: PMC5546723 DOI: 10.1371/journal.pone.0182576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022] Open
Abstract
Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.
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Affiliation(s)
- Chenhui Chang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
| | - Fuzhong Wu
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, 8 Chengdu, China
| | - Wanqin Yang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, 8 Chengdu, China
- * E-mail:
| | - Zhenfeng Xu
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, 8 Chengdu, China
| | - Rui Cao
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
| | - Wei He
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
| | - Bo Tan
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of Yangtze River, 8 Chengdu, China
| | - Meta Francis Justine
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, PR China
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16
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Yamashita S, Hirose D. Phylogenetic analysis of Ganoderma australe complex in a Bornean tropical rainforest and implications for mechanism of coexistence of various phylogenetic types. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Baldrian P, Zrůstová P, Tláskal V, Davidová A, Merhautová V, Vrška T. Fungi associated with decomposing deadwood in a natural beech-dominated forest. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Yang C, Schaefer DA, Liu W, Popescu VD, Yang C, Wang X, Wu C, Yu DW. Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest. Sci Rep 2016; 6:31066. [PMID: 27553882 PMCID: PMC4995510 DOI: 10.1038/srep31066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a ‘pure diversity’ effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world’s stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis.
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Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Douglas A Schaefer
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Weijie Liu
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Viorel D Popescu
- Ohio University, Department of Biological Sciences, 107 Irvine Hall, Athens OH, 45701, USA.,University of Bucharest, Centre for Environmental Research (CCMESI), 1 N Balcescu Blvd., Bucharest, Romania
| | - Chenxue Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
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19
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Purahong W, Arnstadt T, Kahl T, Bauhus J, Kellner H, Hofrichter M, Krüger D, Buscot F, Hoppe B. Are correlations between deadwood fungal community structure, wood physico-chemical properties and lignin-modifying enzymes stable across different geographical regions? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.01.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Wal A, Klein Gunnewiek PJA, Cornelissen JHC, Crowther TW, Boer W. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. Ecosphere 2016. [DOI: 10.1002/ecs2.1393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Annemieke Wal
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
| | - Paulien J. A. Klein Gunnewiek
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
| | - J. Hans C. Cornelissen
- Systems Ecology, Department of Ecological ScienceVU University (Vrije Universiteit) Amsterdam De Boelelaan 1085 1081 HV Amsterdam The Netherlands
| | - Thomas W. Crowther
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6700 AB Wageningen The Netherlands
| | - Wietse Boer
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands
- Department of Soil QualityWageningen University Droevendaalsesteeg 4, Building 104 6708 PB Wageningen The Netherlands
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21
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Trivedi P, Delgado-Baquerizo M, Trivedi C, Hu H, Anderson IC, Jeffries TC, Zhou J, Singh BK. Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships. ISME JOURNAL 2016; 10:2593-2604. [PMID: 27168143 DOI: 10.1038/ismej.2016.65] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/31/2022]
Abstract
A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.
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Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Chanda Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
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