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Feng Y, Xu T, Wang W, Sun S, Zhang M, Song F. Nitrogen addition changed soil fungal community structure and increased the biomass of functional fungi in Korean pine plantations in temperate northeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172349. [PMID: 38615770 DOI: 10.1016/j.scitotenv.2024.172349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Nitrogen (N) deposition is a global environmental issue that can have significant impacts on the community structure and function in ecosystems. Fungi play a key role in soil biogeochemical cycles and their community structures are tightly linked to the health and productivity of forest ecosystems. Based on high-throughput sequencing and ergosterol extraction, we examined the changes in community structure, composition, and biomass of soil ectomycorrhizal (ECM) and saprophytic (SAP) fungi in 0-10 cm soil layer after 8 years of continuous N addition and their driving factors in a temperate Korean pine plantation in northeast China. Our results showed that N addition increased fungal community richness, with the highest richness and Chao1 index under the low N treatment (LN: 20 kg N ha-1 yr-1). Based on the FUN Guild database, we found that the relative abundance of ECM and SAP fungi increased first and then decreased with increasing N deposition concentration. The molecular ecological network analysis showed that the interaction between ECM and SAP fungi was enhanced by N addition, and the interaction was mainly positive in the ECM fungal network. N addition increased fungal biomass, and the total fungal biomass (TFB) was the highest under the MN treatment (6.05 ± 0.3 mg g-1). Overall, we concluded that N addition changed soil biochemical parameters, increased fungal activity, and enhanced functional fungal interactions in the Korean pine plantation over an 8-year simulated N addition. We need to consider the effects of complex soil conditions on soil fungi and emphasize the importance of regulating soil fungal community structure and biomass for managing forest ecosystems. These findings could deepen our understanding of the effects of increased N deposition on soil fungi in temperate forests in northern China, which can provide the theoretical basis for reducing the effects of increased N deposition on forest soil.
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Affiliation(s)
- Yuhan Feng
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Tianle Xu
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Wei Wang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Simiao Sun
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Heilongjiang Academy of Black Soil Conservation & Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Mengmeng Zhang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Fuqiang Song
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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Jomura M, Yoshida R, Michalčíková L, Tláskal V, Baldrian P. Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe. J Fungi (Basel) 2022; 8:jof8070673. [PMID: 35887430 PMCID: PMC9325057 DOI: 10.3390/jof8070673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Dead wood represents an important pool of carbon and nitrogen in forest ecosystems. This source of soil organic matter has diverse ecosystem functions that include, among others, carbon and nitrogen cycling. However, information is limited on how deadwood properties such as chemical composition, decomposer abundance, community composition, and age correlate and affect decomposition rate. Here, we targeted coarse dead wood of beech, spruce, and fir, namely snags and tree trunks (logs) in an old-growth temperate forest in central Europe; measured their decomposition rate as CO2 production in situ; and analyzed their relationships with other measured variables. Respiration rate of dead wood showed strong positive correlation with acid phosphatase activity and negative correlation with lignin content. Fungal biomass (ergosterol content) and moisture content were additional predictors. Our results indicate that dead wood traits, including tree species, age, and position (downed/standing), affected dead wood chemical properties, microbial biomass, moisture condition, and enzyme activity through changes in fungal communities and ultimately influenced the decomposition rate of dead wood.
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Affiliation(s)
- Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
- Correspondence:
| | - Riki Yoshida
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
| | - Lenka Michalčíková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
- Department of Biology, Faculty of Science, University of Hradec Kralove, Hradecká 1285, 500-03 Hradec Králové, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142-20 Prague, Czech Republic; (L.M.); (V.T.); (P.B.)
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Phosphorus and Zinc Are Strongly Associated with Belowground Fungal Communities in Wheat Field under Long-Term Fertilization. Microbiol Spectr 2022; 10:e0011022. [PMID: 35266812 PMCID: PMC9045391 DOI: 10.1128/spectrum.00110-22] [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] [Indexed: 01/04/2023] Open
Abstract
Belowground fungi are closely related to crop growth, and agricultural fertilization is widely known to affect soil fungal communities. Yet it remains unclear whether fungal communities in differing belowground habitats—root endosphere, rhizosphere soil, and bulk soil—respond differently to long-term fertilization. Here we investigated the variation in fungal communities of root endosphere, rhizosphere soil, and bulk soil under 35 years of fertilization in wheat fields. Specifically, the fertilization regimes were applied as five treatments: soils receiving NPK fertilizer, NPK and cow manure (NPK+CM), NPK and pig manure (NPK+PM), NPK and wheat straw (NPK+WS), and no fertilizer (Control). Long-term fertilization significantly impacted fungal community composition in all three habitats, and these effects were stronger in the rhizosphere and bulk soils than root endosphere. Mantel test results showed that fungal community composition was significantly correlated with phosphorus and zinc contents. Further, fungal alpha diversity was lowest in the NPK+PM treatment and was negatively correlated with both phosphorus and zinc contents. Moreover, NPK+PM treatment had the lowest complexity of fungal co-occurrence network, and in general network complexity was significantly negatively correlated with the zinc and phosphorus contents. Taken together, these results suggest that long-term fertilization can impact fungal communities not only in soils but in root endosphere, and this is strongly associated with the contents of phosphorus and zinc there, a finding important for guiding fertilization management practices and supporting sustainable agriculture. IMPORTANCE Fungi, an essential component in nutrient cycling and plant growth, are highly sensitive to fertilization. However, there are limited studies on fungi in root endosphere under long-term fertilization management. Our research extended the study on the endophytic fungal community of crop roots under agricultural management and found that its responses were similar to the communities in soil habitats. In addition, the type of organic materials was reported as the main driver affecting soil fungal community under long-term fertilization. Our research further revealed that the underlying mechanism of affecting the fungal communities in the soils and roots was the differences in phosphorus and zinc contents caused by the application of different organic materials. Therefore, our results highlight that except for phosphorus, zinc content of the organic materials should be considered in long-term organic fertilization systems.
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4
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Zanne AE, Powell JR, Flores-Moreno H, Kiers ET, van 't Padje A, Cornwell WK. Finding fungal ecological strategies: Is recycling an option? FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Presley GN, Zhang J, Purvine SO, Schilling JS. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. Front Microbiol 2020; 11:1646. [PMID: 32849338 PMCID: PMC7399148 DOI: 10.3389/fmicb.2020.01646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023] Open
Abstract
Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
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Affiliation(s)
- Gerald N Presley
- Department of Wood Science and Engineering, Oregon State University, Corvallis, OR, United States
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
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Yang T, Tedersoo L, Lin X, Fitzpatrick MC, Jia Y, Liu X, Ni Y, Shi Y, Lu P, Zhu J, Chu H. Distinct fungal successional trajectories following wildfire between soil horizons in a cold-temperate forest. THE NEW PHYTOLOGIST 2020; 227:572-587. [PMID: 32155671 DOI: 10.1111/nph.16531] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Soil fungi represent a major component of below-ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving mechanisms following wildfire remain unclear. We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) along a near-complete fire chronosequence (1, 2, 8, 14, 30, 49 and c. 260 yr) in cold-temperate forests of the Great Khingan Mountains, China. The importance of soil properties, spatial distance and tree composition were also tested. Ectomycorrhizal fungal richness and β-glucosidase activity were strongly reduced by burning and significantly increased with 'time since fire' in the Oe horizon but not in the mineral horizons. Time since fire and soil C : N ratio were the primary drivers of fungal composition in the Oe and A1/A2 horizons, respectively. Ectomycorrhizal fungal composition was remarkably sensitive to fire history in the Oe horizon, while saprotroph community was strongly affected by time since fire in the deeper soil horizon and this effect emerged 18 years after fire in the A2 horizon. Our study demonstrates pronounced horizon-dependent successional trajectories following wildfire and indicates interactive effects of time since fire, soil stoichiometry and spatial distance in the reassembly of below-ground fungal communities in a cold and fire-prone region.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
| | - Xingwu Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Centre for Environmental Science, Frostburg, MD, 21531, USA
| | - Yunsheng Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Pengpeng Lu
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xiying Road 76, Xi'an, 710043, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
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7
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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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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9
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Jia Y, Gu D, Wu C, Yang W, Du X, Wen T, Lv Y, Kong X, Tian X. Nitrogen deposition slows down the litter decomposition induced by soil macrofauna in the soil of subtropical forests in China. Ecol Res 2019. [DOI: 10.1111/1440-1703.1277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Jia
- Huaiyin Institute of Agricultural Sciences Huaian China
- School of Life SciencesNanjing University Nanjing China
| | - Dalu Gu
- Huaiyin Institute of Agricultural Sciences Huaian China
| | - Chuanwan Wu
- Huaiyin Institute of Agricultural Sciences Huaian China
| | - Wenfei Yang
- Huaiyin Institute of Agricultural Sciences Huaian China
| | - Xiaofeng Du
- Huaiyin Institute of Agricultural Sciences Huaian China
| | - Tinggang Wen
- Huaiyin Institute of Agricultural Sciences Huaian China
| | - Yanna Lv
- School of Pharmacy and Biological SciencesWeifang Medical University Weifang China
| | - Xiangshi Kong
- School of Life SciencesNanjing University Nanjing China
| | - Xingjun Tian
- School of Life SciencesNanjing University Nanjing China
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10
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Chen Y, Liu Y, Zhang J, Yang W, He R, Deng C. Microclimate exerts greater control over litter decomposition and enzyme activity than litter quality in an alpine forest-tundra ecotone. Sci Rep 2018; 8:14998. [PMID: 30301949 PMCID: PMC6177423 DOI: 10.1038/s41598-018-33186-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Plant litter decomposition is an important biogeochemical process in terrestrial ecosystems. Although climate and substrate quality controls over litter decomposition are reasonably well understood, their impacts on lignocellulose degradation and lignocellulolytic enzymes remain elusive. Here, the decomposition of three leaf litters derived from Salix paraplesia (SP), Deyeuxia scabrescens (DS), and Ajuga ovalifolia (AO), was studied across an alpine forest-tundra ecotone during one snow-covered season with the objective of distinguishing between the effects of microclimate and litter quality on litter decomposition rates and lignocellulolytic enzymes. The results showed that both microclimate and litter quality affected lignocellulose degradation rates and lignocellulolytic enzyme activities; however, microclimate factors had the greater effects. Interestingly, freeze-thaw cycles and moisture were the predominant factors explaining the variations in decomposition rate and enzyme activities. Higher cellulose degradation rates were associated with higher cellulose concentrations. Cellulolytic enzymes had a greater effect on litter decomposition than did ligninolytic enzymes at the early decomposition stage. Litter decomposition and enzyme activities should be given more attention under global climate change, as the direction and magnitude of changes in microclimate factors and litter quality could strongly influence the nutrient cycling and energy fluxes of alpine ecosystems.
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Affiliation(s)
- Yamei Chen
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Liu
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China.
| | - Jian Zhang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Wanqin Yang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Runlian He
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Changchun Deng
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
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Abstract
Decomposer fungi continually deplete the organic resources they inhabit, so successful colonization of new resources is a crucial part of their ecology. Colonization success can be split into (i) the ability to arrive at, gain entry into, and establish within a resource and (ii) the ability to persist within the resource until reproduction and dissemination. Fungi vary in their life history strategies, the three main drivers of which are stress (S-selected), disturbance (ruderal, or R-selected), and incidence of competitors (C-selected); however, fungi often have combinations of characteristics from different strategies. Arrival at a new resource may occur as spores or mycelium, with successful entry and establishment (primary resource capture) within the resource largely dependent on the enzymatic ability of the fungus. The communities that develop in a newly available resource depend on environmental conditions and, in particular, the levels of abiotic stress present (e.g., high temperature, low water availability). Community change occurs when these initial colonizers are replaced by species that are either more combative (secondary resource capture) or better able to tolerate conditions within the resource, either through changing abiotic conditions or due to modification of the resource by the initial colonizers. Competition for territory may involve highly specialized species-specific interactions such as mycoparasitism or may be more general; in both cases combat involves changes in morphology, metabolism, and reactive oxygen species production, and outcomes of these interactions can be altered under different environmental conditions. In summary, community development is not a simple ordered sequence, but a complex ever-changing mosaic.
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12
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Navrátilová D, Větrovský T, Baldrian P. Spatial heterogeneity of cellulolytic activity and fungal communities within individual decomposing Quercus petraea leaves. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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de Menezes AB, Richardson AE, Thrall PH. Linking fungal–bacterial co-occurrences to soil ecosystem function. Curr Opin Microbiol 2017; 37:135-141. [DOI: 10.1016/j.mib.2017.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/21/2017] [Indexed: 02/04/2023]
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14
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Boddy L, Hiscox J, Gilmartin EC, Johnston SR, Heilmann-Clausen J. Chapter 12 Wood Decay Communities in Angiosperm Wood. Mycology 2017. [DOI: 10.1201/9781315119496-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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15
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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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16
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Hortal S, Powell JR, Plett JM, Simonin A, Anderson IC. Intraspecific competition between ectomycorrhizal Pisolithus microcarpus isolates impacts plant and fungal performance under elevated CO2 and temperature. FEMS Microbiol Ecol 2016; 92:fiw113. [PMID: 27222224 DOI: 10.1093/femsec/fiw113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2016] [Indexed: 11/14/2022] Open
Abstract
Root systems are simultaneously colonized by multiple individuals of mycorrhizal fungi. Intraspecific competitive interactions between fungal isolates are likely to affect both fungal and plant performance and be influenced by abiotic factors. Here, we assessed the impact of intraspecific competition between three Pisolithus microcarpus isolates on the establishment of, and benefit derived from, symbioses with Eucalyptus grandis seedlings. We investigated the outcomes of competition under ambient and elevated temperature and CO2 concentration ([CO2]) in a factorial design. We observed a reduction in mycelium growth, mycorrhiza formation and seedling mass when two P. microcarpus isolates were co-inoculated on a single E. grandis seedling. Isolates invested more in mycelium than in mycorrhizas in the presence of a competitor. All isolates responded negatively to elevated [CO2] and positively to elevated temperature, which led to no changes on the outcomes of the interactions with changing conditions. However, the presence of a competitor hindered the positive response of P. microcarpus isolates to warming, which resulted in larger negative effects of competition under elevated temperature than under ambient conditions. Our study highlights the need to consider how competition affects individual fungal responses as well as plant performance when trying to predict the impacts of climate change.
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Affiliation(s)
- S Hortal
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - J R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - J M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - A Simonin
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - I C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
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17
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Divya L, Sadasivan C. Trichoderma viride Laccase Plays a Crucial Role in Defense Mechanism against Antagonistic Organisms. Front Microbiol 2016; 7:741. [PMID: 27242756 PMCID: PMC4868839 DOI: 10.3389/fmicb.2016.00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/03/2016] [Indexed: 11/13/2022] Open
Abstract
Fungal laccases are involved in a variety of physiological functions such as delignification, morphogenesis, and parasitism. In addition to these functions, we suggest that fungal laccases are involved in defense mechanisms. When the laccase secreting Trichoderma viride was grown in the presence of a range of microorganisms including bacteria and fungi, laccase secretion was enhanced in response to antagonistic organisms alone. In addition, growth of antagonistic microbes was restricted by the secreting fungi. Besides, our study for the first time shows the inability of the secreting fungi (T. viride) to compete with antagonistic organism when laccase activity is inhibited, further emphasizing its involvement in rendering a survival advantage to the secreting organism. When laccase inhibitor was added to the media, the zone of inhibition exerted by the antagonist organism was more pronounced and consequently growth of T. viride was significantly restricted. Based on these observations we accentuate that, laccase plays an important role in defense mechanism and provides endurance to the organism when encountered with an antagonistic organism in its surrounding.
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Affiliation(s)
| | - C. Sadasivan
- Department of Biotechnology and Microbiology, Kannur UniversityKannur, India
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18
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Fungal Communities in Soils: Soil Organic Matter Degradation. Methods Mol Biol 2016. [PMID: 26791498 DOI: 10.1007/978-1-4939-3369-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of fungal community members involved in a particular decomposition process. Further information can be gained through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual fungal taxa. Here we describe the use of these methods to explore the cellulolytic fungal community in forest litter and soil.
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19
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Toward Modeling the Resistance and Resilience of "Below-ground" Fungal Communities: A Mechanistic and Trait-Based Approach. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:1-44. [PMID: 26505687 DOI: 10.1016/bs.aambs.2015.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The role of fungi in shaping ecosystems is well evidenced and there is growing recognition of their importance among scientists and the general public. Establishing and separating the role of key local (soil chemical, biological, and physical properties) and global (climate, dispersal limitation) drivers in fungal community structure and functioning is currently a source of frustration to mycologists. The quest to determine niche processes and environmental characteristics shaping fungal community structure, known to be important for plant and animal communities, is proving difficult, resulting in the acknowledgment that niche neutral processes (climate, dispersal limitations) may dominate. The search for predictable patterns in fungal community structure may have been restricted as the "appropriate" scales at which to measure community structure and characterize the environment have not been fully determined yet, and the focus on taxonomy makes it difficult to link environmental characteristics to fungal traits. While key determinants of microbial community composition have been uncovered for some functional groups, the differential response of functional groups is largely unknown. Before we can truly understand what drives the development of microbial community structure, an understanding of the autecology of major fungal taxa and how they interact with their immediate environment (from the micro- up to kilometer scale) is urgently needed. Furthermore, key information and empirical data is missing at the microscale due to experimental difficulties in mapping this heterogeneous and opaque environment. We therefore present a framework that would help generate this much-needed empirical data and information at the microscale, together with modeling approaches to link the spatial and temporal scales. The latter is important as we propose that there is much to be gained by linking our understanding of fungal community responses across scales, in order to develop species and community-environment-function predictive models.
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20
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Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0341-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Simeng Z, Sacha G, Isabelle HG, Marie-Noëlle R. A PCR-based method to quantify fungal growth during pretreatment of lignocellulosic biomass. J Microbiol Methods 2015; 115:67-70. [DOI: 10.1016/j.mimet.2015.05.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/28/2022]
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22
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Song Z, Vail A, Sadowsky MJ, Schilling JS. Influence of Hyphal Inoculum potential on the Competitive Success of Fungi Colonizing Wood. MICROBIAL ECOLOGY 2015; 69:758-67. [PMID: 25750000 DOI: 10.1007/s00248-015-0588-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 02/18/2015] [Indexed: 05/28/2023]
Abstract
The relative amounts of hyphal inoculum in forest soils may determine the capacity for fungi to compete with and replace early colonizers of wood in ground contact. Our aim in this study was to test the flexibility of priority effects (colonization timing) by varying the timing of inoculum introduction (i.e., precolonization) and amount of inoculum (i.e., inoculum potential). We controlled these variables in soil-block microcosms using fungi with known competitive outcomes in similar conditions, tracking isolate-specific fungal biomass, and residue physiochemistry over time. In the precolonization trial (experiment I), a brown rot fungus Gloeophyllum trabeum was given 1, 3, or 5 weeks to precolonize wood blocks (oak, birch, pine, and spruce) prior the introduction of a white rot fungus, Irpex lacteus, a more aggressive colonizer in this set-up. In the inoculum potential trial (experiment II), the fungi were inoculated simultaneously, but with eightfold higher brown rot inoculum than that of experiment I. As expected, longer precolonization duration increased the chance for the less-competitive brown rot fungus to outcompete its white rot opponent. Higher brown rot fungal inoculum outside of the wood matrix also resulted in competitive success for the brown rot isolate in most cases. These temporal shifts in fungal dominance were detectable in a 'community snapshot' as isolate-specific quantitative PCR, but also as functionally-relevant consequences of wood rot type, including carbohydrate depolymerization and pH. These results from a controlled system reinforce fungal-fungal interaction and suggest that relative inoculum availability beyond the wood matrix (i.e., soils) might regulate the duration of priority effects and shift the functional trajectory of wood decomposition.
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Affiliation(s)
- Zewei Song
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 2004 Folwell Avenue, St. Paul, MN, 55108, USA
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23
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Willers C, Jansen van Rensburg P, Claassens S. Microbial signature lipid biomarker analysis - an approach that is still preferred, even amid various method modifications. J Appl Microbiol 2015; 118:1251-63. [PMID: 25765073 DOI: 10.1111/jam.12798] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 11/26/2022]
Affiliation(s)
- C. Willers
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
| | | | - S. Claassens
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
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24
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Crowther TW, Maynard DS, Crowther TR, Peccia J, Smith JR, Bradford MA. Untangling the fungal niche: the trait-based approach. Front Microbiol 2014; 5:579. [PMID: 25400630 PMCID: PMC4215788 DOI: 10.3389/fmicb.2014.00579] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/14/2014] [Indexed: 11/26/2022] Open
Abstract
Fungi are prominent components of most terrestrial ecosystems, both in terms of biomass and ecosystem functioning, but the hyper-diverse nature of most communities has obscured the search for unifying principles governing community organization. In particular, unlike plants and animals, observational studies provide little evidence for the existence of niche processes in structuring fungal communities at broad spatial scales. This limits our capacity to predict how communities, and their functioning, vary across landscapes. We outline how a shift in focus, from taxonomy toward functional traits, might prove to be valuable in the search for general patterns in fungal ecology. We build on theoretical advances in plant and animal ecology to provide an empirical framework for a trait-based approach in fungal community ecology. Drawing upon specific characteristics of the fungal system, we highlight the significance of drought stress and combat in structuring free-living fungal communities. We propose a conceptual model to formalize how trade-offs between stress-tolerance and combative dominance are likely to organize communities across environmental gradients. Given that the survival of a fungus in a given environment is contingent on its ability to tolerate antagonistic competitors, measuring variation in combat trait expression along environmental gradients provides a means of elucidating realized, from fundamental niche spaces. We conclude that, using a trait-based understanding of how niche processes structure fungal communities across time and space, we can ultimately link communities with ecosystem functioning. Our trait-based framework highlights fundamental uncertainties that require testing in the fungal system, given their potential to uncover general mechanisms in fungal ecology.
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Affiliation(s)
- Thomas W. Crowther
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | - Daniel S. Maynard
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | | | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale UniversityNew Haven, CT, USA
| | - Jeffrey R. Smith
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | - Mark A. Bradford
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
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25
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Štursová M, Šnajdr J, Cajthaml T, Bárta J, Šantrůčková H, Baldrian P. When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback. THE ISME JOURNAL 2014; 8:1920-31. [PMID: 24671082 PMCID: PMC4139728 DOI: 10.1038/ismej.2014.37] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 01/24/2014] [Accepted: 02/10/2014] [Indexed: 11/09/2022]
Abstract
Coniferous forests cover extensive areas of the boreal and temperate zones. Owing to their primary production and C storage, they have an important role in the global carbon balance. Forest disturbances such as forest fires, windthrows or insect pest outbreaks have a substantial effect on the functioning of these ecosystems. Recent decades have seen an increase in the areas affected by disturbances in both North America and Europe, with indications that this increase is due to both local human activity and global climate change. Here we examine the structural and functional response of the litter and soil microbial community in a Picea abies forest to tree dieback following an invasion of the bark beetle Ips typographus, with a specific focus on the fungal community. The insect-induced disturbance rapidly and profoundly changed vegetation and nutrient availability by killing spruce trees so that the readily available root exudates were replaced by more recalcitrant, polymeric plant biomass components. Owing to the dramatic decrease in photosynthesis, the rate of decomposition processes in the ecosystem decreased as soon as the one-time litter input had been processed. The fungal community showed profound changes, including a decrease in biomass (2.5-fold in the litter and 12-fold in the soil) together with the disappearance of fungi symbiotic with tree roots and a relative increase in saprotrophic taxa. Within the latter group, successive changes reflected the changing availability of needle litter and woody debris. Bacterial biomass appeared to be either unaffected or increased after the disturbance, resulting in a substantial increase in the bacterial/fungal biomass ratio.
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Affiliation(s)
- Martina Štursová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, Praha 4, Czech Republic
| | - Jaroslav Šnajdr
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, Praha 4, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, Praha 4, Czech Republic
| | - Jiří Bárta
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, Praha 4, Czech Republic
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26
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A'Bear AD, Jones TH, Boddy L. Potential impacts of climate change on interactions among saprotrophic cord-forming fungal mycelia and grazing soil invertebrates. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2013.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Baldrian P, Větrovský T, Cajthaml T, Dobiášová P, Petránková M, Šnajdr J, Eichlerová I. Estimation of fungal biomass in forest litter and soil. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.10.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Hahn F, Ullrich R, Hofrichter M, Liers C. Experimental approach to follow the spatiotemporal wood degradation in fungal microcosms. Biotechnol J 2012; 8:127-32. [DOI: 10.1002/biot.201200183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/14/2012] [Accepted: 07/10/2012] [Indexed: 11/06/2022]
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29
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Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization. Appl Environ Microbiol 2012; 78:6078-86. [PMID: 22729539 DOI: 10.1128/aem.01091-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.
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30
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Štursová M, Žifčáková L, Leigh MB, Burgess R, Baldrian P. Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 2012; 80:735-46. [DOI: 10.1111/j.1574-6941.2012.01343.x] [Citation(s) in RCA: 305] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology; Institute of Microbiology ASCR; Prague; Czech Republic
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology; Institute of Microbiology ASCR; Prague; Czech Republic
| | - Mary Beth Leigh
- Institute of Arctic Biology; University of Alaska Fairbanks; Fairbanks; AK; USA
| | - Robert Burgess
- Institute of Arctic Biology; University of Alaska Fairbanks; Fairbanks; AK; USA
| | - Petr Baldrian
- Laboratory of Environmental Microbiology; Institute of Microbiology ASCR; Prague; Czech Republic
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31
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Baldrian P, Kolařík M, Stursová M, Kopecký J, Valášková V, Větrovský T, Zifčáková L, Snajdr J, Rídl J, Vlček C, Voříšková J. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. THE ISME JOURNAL 2012; 6:248-58. [PMID: 21776033 PMCID: PMC3260513 DOI: 10.1038/ismej.2011.95] [Citation(s) in RCA: 428] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/16/2011] [Accepted: 06/20/2011] [Indexed: 11/09/2022]
Abstract
Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídeňská, Praha, Czech Republic.
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