1
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Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD. Ectomycorrhizal fungi are more sensitive to high soil nitrogen levels in forests exposed to nitrogen deposition. New Phytol 2024; 242:1725-1738. [PMID: 38213001 DOI: 10.1111/nph.19509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Ectomycorrhizal fungi are essential for nitrogen (N) cycling in many temperate forests and responsive to anthropogenic N addition, which generally decreases host carbon (C) allocation to the fungi. In the boreal region, however, ectomycorrhizal fungal biomass has been found to correlate positively with soil N availability. Still, responses to anthropogenic N input, for instance through atmospheric deposition, are commonly negative. To elucidate whether variation in N supply affects ectomycorrhizal fungi differently depending on geographical context, we investigated ectomycorrhizal fungal communities along fertility gradients located in two nemo-boreal forest regions with similar ranges in soil N : C ratios and inorganic N availability but contrasting rates of N deposition. Ectomycorrhizal biomass and community composition remained relatively stable across the N gradient with low atmospheric N deposition, but biomass decreased and the community changed more drastically with increasing N availability in the gradient subjected to higher rates of N deposition. Moreover, potential activities of enzymes involved in ectomycorrhizal mobilisation of organic N decreased as N availability increased. In forests with low external input, we propose that stabilising feedbacks in tree-fungal interactions maintain ectomycorrhizal fungal biomass and communities even in N-rich soils. By contrast, anthropogenic N input seems to impair ectomycorrhizal functions.
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Affiliation(s)
- Karolina Jörgensen
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-750 07, Uppsala, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Håkan Wallander
- Department of Biology, Lund University, Sölvegatan 37, 223 26, Lund, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-750 07, Uppsala, Sweden
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2
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Castaño C, Hallin S, Egelkraut D, Lindahl BD, Olofsson J, Clemmensen KE. Contrasting plant-soil-microbial feedbacks stabilize vegetation types and uncouple topsoil C and N stocks across a subarctic-alpine landscape. New Phytol 2023; 238:2621-2633. [PMID: 36519258 DOI: 10.1111/nph.18679] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/02/2022] [Indexed: 05/19/2023]
Abstract
Global vegetation regimes vary in belowground carbon (C) and nitrogen (N) dynamics. However, disentangling large-scale climatic controls from the effects of intrinsic plant-soil-microbial feedbacks on belowground processes is challenging. In local gradients with similar pedo-climatic conditions, effects of plant-microbial feedbacks may be isolated from large-scale drivers. Across a subarctic-alpine mosaic of historic grazing fields and surrounding heath and birch forest, we evaluated whether vegetation-specific plant-microbial feedbacks involved contrasting N cycling characteristics and C and N stocks in the organic topsoil. We sequenced soil fungi, quantified functional genes within the inorganic N cycle, and measured 15 N natural abundance. In grassland soils, large N stocks and low C : N ratios associated with fungal saprotrophs, archaeal ammonia oxidizers, and bacteria capable of respiratory ammonification, indicating maintained inorganic N cycling a century after abandoned reindeer grazing. Toward forest and heath, increasing abundance of mycorrhizal fungi co-occurred with transition to organic N cycling. However, ectomycorrhizal fungal decomposers correlated with small soil N and C stocks in forest, while root-associated ascomycetes associated with small N but large C stocks in heath, uncoupling C and N storage across vegetation types. We propose that contrasting, positive plant-microbial feedbacks stabilize vegetation trajectories, resulting in diverging soil C : N ratios at the landscape scale.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Dagmar Egelkraut
- Department of Biological Sciences, University of Bergen, 5006, Bergen, Norway
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Johan Olofsson
- Department of Ecology and Environmental Science, Umeå University, 90187, Umeå, Sweden
| | - Karina Engelbrecht Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
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3
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Pérez‐Izquierdo L, Bengtsson J, Clemmensen KE, Granath G, Gundale MJ, Ibáñez TS, Lindahl BD, Strengbom J, Taylor A, Viketoft M, Wardle DA, Nilsson M. Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests. Ecol Evol 2023; 13:e10086. [PMID: 37206687 PMCID: PMC10191780 DOI: 10.1002/ece3.10086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023] Open
Abstract
Changes in fire regime of boreal forests in response to climate warming are expected to impact postfire recovery. However, quantitative data on how managed forests sustain and recover from recent fire disturbance are limited.Two years after a large wildfire in managed even-aged boreal forests in Sweden, we investigated how recovery of aboveground and belowground communities, that is, understory vegetation and soil microbial and faunal communities, responded to variation in the severity of soil (i.e., consumption of soil organic matter) and canopy fires (i.e., tree mortality).While fire overall enhanced diversity of understory vegetation through colonization of fire adapted plant species, it reduced the abundance and diversity of soil biota. We observed contrasting effects of tree- and soil-related fire severity on survival and recovery of understory vegetation and soil biological communities. Severe fires that killed overstory Pinus sylvestris promoted a successional stage dominated by the mosses Ceratodon purpureus and Polytrichum juniperinum, but reduced regeneration of tree seedlings and disfavored the ericaceous dwarf-shrub Vaccinium vitis-idaea and the grass Deschampsia flexuosa. Moreover, high tree mortality from fire reduced fungal biomass and changed fungal community composition, in particular that of ectomycorrhizal fungi, and reduced the fungivorous soil Oribatida. In contrast, soil-related fire severity had little impact on vegetation composition, fungal communities, and soil animals. Bacterial communities responded to both tree- and soil-related fire severity. Synthesis: Our results 2 years postfire suggest that a change in fire regime from a historically low-severity ground fire regime, with fires that mainly burns into the soil organic layer, to a stand-replacing fire regime with a high degree of tree mortality, as may be expected with climate change, is likely to impact the short-term recovery of stand structure and above- and belowground species composition of even-aged P. sylvestris boreal forests.
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Affiliation(s)
| | - Jan Bengtsson
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant PathologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Gustaf Granath
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Michael J. Gundale
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Theresa S. Ibáñez
- Department of WildlifeFish and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Joachim Strengbom
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Astrid Taylor
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Maria Viketoft
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - David A. Wardle
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | - Marie‐Charlotte Nilsson
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
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4
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Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD. Do ectomycorrhizal exploration types reflect mycelial foraging strategies? New Phytol 2023; 237:576-584. [PMID: 36271619 PMCID: PMC10098516 DOI: 10.1111/nph.18566] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/01/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizal exploration types are commonly assumed to denote spatial foraging patterns and resource-related niches of extraradical mycelia. However, empirical evidence of the consistency of foraging strategies within exploration types is lacking. Here, we analysed ectomycorrhizal foraging patterns by incubating root-excluding ingrowth mesh bags filled with six different substrates in mature Picea abies forests. High-throughput sequencing was used to characterise ectomycorrhizal fungal communities in the mesh bags and on adjacent fine roots after one growing season. Contrary to expectations, many ectomycorrhizal genera of exploration types that are thought to produce little extraradical mycelium colonised ingrowth bags extensively, whereas genera commonly associated with ample mycelial production occurred sparsely in ingrowth bags relative to their abundance on roots. Previous assumptions about soil foraging patterns of exploration types do not seem to hold. Instead, we propose that variation in the proliferation of extraradical mycelium is related to intergeneric differences in mycelial longevity and the mobility of targeted resources.
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Affiliation(s)
- Karolina Jörgensen
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
- Department of Biological SciencesUniversity of BergenBox 7803NO‐5020BergenNorway
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesBox 7026SE‐750 07UppsalaSweden
| | - Håkan Wallander
- Department of BiologyLund UniversitySölvegatan 37223 26LundSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
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5
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Clemmensen KE, Ihrmark K, Durling MB, Lindahl BD. Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons. Methods Mol Biol 2022; 2605:37-64. [PMID: 36520388 DOI: 10.1007/978-1-0716-2871-3_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fungal species participate in vast numbers of processes in the landscape around us. However, their cryptic mycelial growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enables identification and relative quantification of fungal community members across well-replicated experimental settings.Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, i.e., the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon pool to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.
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Affiliation(s)
- Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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6
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Fanin N, Clemmensen KE, Lindahl BD, Farrell M, Nilsson MC, Gundale MJ, Kardol P, Wardle DA. Ericoid shrubs shape fungal communities and suppress organic matter decomposition in boreal forests. New Phytol 2022; 236:684-697. [PMID: 35779014 DOI: 10.1111/nph.18353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Mycorrhizal fungi associated with boreal trees and ericaceous shrubs are central actors in organic matter (OM) accumulation through their belowground carbon allocation, their potential capacity to mine organic matter for nitrogen (N) and their ability to suppress saprotrophs. Yet, interactions between co-occurring ectomycorrhizal fungi (EMF), ericoid mycorrhizal fungi (ERI), and saprotrophs are poorly understood. We used a long-term (19 yr) plant functional group manipulation experiment with removals of tree roots, ericaceous shrubs and mosses and analysed the responses of different fungal guilds (assessed by metabarcoding) and their interactions in relation to OM quality (assessed by mid-infrared spectroscopy and nuclear magnetic resonance) and decomposition (litter mesh-bags) across a 5000-yr post-fire boreal forest chronosequence. We found that the removal of ericaceous shrubs and associated ERI changed the composition of EMF communities, with larger effects occurring at earlier stages of the chronosequence. Removal of shrubs was associated with enhanced N availability, litter decomposition and enrichment of the recalcitrant OM fraction. We conclude that increasing abundance of slow-growing ericaceous shrubs and the associated fungi contributes to increasing nutrient limitation, impaired decomposition and progressive OM accumulation in boreal forests, particularly towards later successional stages. These results are indicative of the contrasting roles of EMF and ERI in regulating belowground OM storage.
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Affiliation(s)
- Nicolas Fanin
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83, Umeå, Sweden
- INRAE, Bordeaux Sciences Agro, UMR 1391 ISPA, 71 avenue Edouard Bourlaux, CS 20032, F33882, Villenave-d'Ornon cedex, France
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-75007, Uppsala, Sweden
| | - Mark Farrell
- CSIRO Agriculture & Food, Kaurna Country, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Marie-Charlotte Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83, Umeå, Sweden
| | - Michael J Gundale
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83, Umeå, Sweden
| | - Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83, Umeå, Sweden
| | - David A Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83, Umeå, Sweden
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore City, 639798, Singapore
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7
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Jörgensen K, Granath G, Strengbom J, Lindahl BD. Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karolina Jörgensen
- Department of Soil and Environment Swedish University of Agricultural Sciences Uppsala Sweden
| | - Gustaf Granath
- Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Joachim Strengbom
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Uppsala Sweden
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8
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Faticov M, Abdelfattah A, Roslin T, Vacher C, Hambäck P, Blanchet FG, Lindahl BD, Tack AJM. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. New Phytol 2021; 231:1770-1783. [PMID: 33960441 DOI: 10.1111/nph.17434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/15/2021] [Indexed: 05/13/2023]
Abstract
Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming × genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.
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Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, A-8010, Austria
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, Uppsala, SE-756 51, Sweden
| | | | - Peter Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - F Guillaume Blanchet
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département de Mathématique, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC, J1H 5N4, Canada
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, SE-750 07, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
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9
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Hasby FA, Barbi F, Manzoni S, Lindahl BD. Transcriptomic markers of fungal growth, respiration and carbon-use efficiency. FEMS Microbiol Lett 2021; 368:6335482. [PMID: 34338746 PMCID: PMC8374604 DOI: 10.1093/femsle/fnab100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-β-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach.
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Affiliation(s)
- Fahri A Hasby
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala SE-75007, Sweden
| | - Florian Barbi
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 8, Stockholm, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala SE-75007, Sweden
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10
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Lindahl BD, Kyaschenko J, Varenius K, Clemmensen KE, Dahlberg A, Karltun E, Stendahl J. A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest. Ecol Lett 2021; 24:1341-1351. [PMID: 33934481 DOI: 10.1111/ele.13746] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
Boreal forest soils are important global carbon sinks, with significant storage in the organic topsoil. Decomposition of these stocks requires oxidative enzymes, uniquely produced by fungi. Across Swedish boreal forests, we found that local carbon storage in the organic topsoil was 33% lower in the presence of a group of closely related species of ectomycorrhizal fungi - Cortinarius acutus s.l.. This observation challenges the prevailing view that ectomycorrhizal fungi generally act to increase carbon storage in soils but supports the idea that certain ectomycorrhizal fungi can complement free-living decomposers, maintaining organic matter turnover, nutrient cycling and tree productivity under nutrient-poor conditions. The indication that a narrow group of fungi may exert a major influence on carbon cycling questions the prevailing dogma of functional redundancy among microbial decomposers. Cortinarius acutus s.l. responds negatively to stand-replacing disturbance, and associated population declines are likely to increase soil carbon sequestration while impeding long-term nutrient cycling.
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Affiliation(s)
- Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Julia Kyaschenko
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Varenius
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Karltun
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Stendahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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11
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Clemmensen KE, Durling MB, Michelsen A, Hallin S, Finlay RD, Lindahl BD. A tipping point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen. Ecol Lett 2021; 24:1193-1204. [PMID: 33754469 DOI: 10.1111/ele.13735] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/19/2020] [Accepted: 02/23/2021] [Indexed: 01/04/2023]
Abstract
Tundra ecosystems are global belowground sinks for atmospheric CO2 . Ongoing warming-induced encroachment by shrubs and trees risks turning this sink into a CO2 source, resulting in a positive feedback on climate warming. To advance mechanistic understanding of how shifts in mycorrhizal types affect long-term carbon (C) and nitrogen (N) stocks, we studied small-scale soil depth profiles of fungal communities and C-N dynamics across a subarctic-alpine forest-heath vegetation gradient. Belowground organic stocks decreased abruptly at the transition from heath to forest, linked to the presence of certain tree-associated ectomycorrhizal fungi that contribute to decomposition when mining N from organic matter. In contrast, ericoid mycorrhizal plants and fungi were associated with organic matter accumulation and slow decomposition. If climatic controls on arctic-alpine forest lines are relaxed, increased decomposition will likely outbalance increased plant productivity, decreasing the overall C sink capacity of displaced tundra.
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Affiliation(s)
- Karina Engelbrecht Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, 750 07, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, 750 07, Sweden
| | - Anders Michelsen
- Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, 750 07, Sweden
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, 750 07, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, Uppsala, 750 07, Sweden
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12
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Kõljalg U, Nilsson HR, Schigel D, Tedersoo L, Larsson KH, May TW, Taylor AFS, Jeppesen TS, Frøslev TG, Lindahl BD, Põldmaa K, Saar I, Suija A, Savchenko A, Yatsiuk I, Adojaan K, Ivanov F, Piirmann T, Pöhönen R, Zirk A, Abarenkov K. The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. Microorganisms 2020; 8:E1910. [PMID: 33266327 PMCID: PMC7760934 DOI: 10.3390/microorganisms8121910] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022] Open
Abstract
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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Affiliation(s)
- Urmas Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Henrik R. Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Dmitry Schigel
- Global Biodiversity Information Facility, 2100 Copenhagen, Denmark; (D.S.); (T.S.J.)
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Karl-Henrik Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia;
| | - Andy F. S. Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK;
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | | | | | - Björn D. Lindahl
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden;
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Ave Suija
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Kristjan Adojaan
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Timo Piirmann
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Raivo Pöhönen
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Allan Zirk
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
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Castaño C, Berlin A, Brandström Durling M, Ihrmark K, Lindahl BD, Stenlid J, Clemmensen KE, Olson Å. Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities. New Phytol 2020; 228:1149-1158. [PMID: 32531109 DOI: 10.1111/nph.16731] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Katharina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
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Martin FM, Dickie I, Lindahl BD, Lennon S, Öpik M, Polle A, Requena N, Selosse MA, Koide RT, Jakobsen I, Watts-Williams SJ, Cavagnaro TR. A tribute to Sally E. Smith. New Phytol 2020; 228:397-402. [PMID: 33460160 DOI: 10.1111/nph.16895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Francis M Martin
- Lab of Excellence ARBRE, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Micro-organismes', INRAE, 54280, Champenoux, France
| | - Ian Dickie
- College of Science, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, 750 07, Uppsala, Sweden
| | - Sarah Lennon
- New Phytologist Central Office, Bailrigg House, Lancaster University, Lancaster, LA1 4YE, UK
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Andrea Polle
- Department of Forest Botany and Tree Physiology, Buesgen-Institute and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, 37077, Germany
| | - Natalia Requena
- Molecular Phytopathology Department, Karlsruhe Institute of Technology, Fritz Haber-Weg 4, Geb. 30.43, 2. OG, D-76131, Karlsruhe, Germany
| | - Marc-André Selosse
- Département Systématique et Evolution, UMR 7205 ISYEB CP 50, Muséum national d'Histoire naturelle, 45 rue Buffon, Paris, 75005, France
- Faculty of Biology, University of Gdansk, ul. Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Iver Jakobsen
- Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stephanie J Watts-Williams
- School of Agriculture, Food & Wine and the Waite Research Institute, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Timothy R Cavagnaro
- School of Agriculture, Food & Wine and the Waite Research Institute, The University of Adelaide, Urrbrae, SA, 5064, Australia
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15
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Parker TC, Clemmensen KE, Friggens NL, Hartley IP, Johnson D, Lindahl BD, Olofsson J, Siewert MB, Street LE, Subke JA, Wookey PA. Rhizosphere allocation by canopy-forming species dominates soil CO 2 efflux in a subarctic landscape. New Phytol 2020; 227:1818-1830. [PMID: 32248524 DOI: 10.1111/nph.16573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
In arctic ecosystems, climate change has increased plant productivity. As arctic carbon (C) stocks predominantly are located belowground, the effects of greater plant productivity on soil C storage will significantly determine the net sink/source potential of these ecosystems, but vegetation controls on soil CO2 efflux remain poorly resolved. In order to identify the role of canopy-forming species in belowground C dynamics, we conducted a girdling experiment with plots distributed across 1 km2 of treeline birch (Betula pubescens) forest and willow (Salix lapponum) patches in northern Sweden and quantified the contribution of canopy vegetation to soil CO2 fluxes and belowground productivity. Girdling birches reduced total soil CO2 efflux in the peak growing season by 53%, which is double the expected amount, given that trees contribute only half of the total leaf area in the forest. Root and mycorrhizal mycelial production also decreased substantially. At peak season, willow shrubs contributed 38% to soil CO2 efflux in their patches. Our findings indicate that C, recently fixed by trees and tall shrubs, makes a substantial contribution to soil respiration. It is critically important that these processes are taken into consideration in the context of a greening arctic because productivity and ecosystem C sequestration are not synonymous.
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Affiliation(s)
- Thomas C Parker
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Nina L Friggens
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Iain P Hartley
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter,, EX4 4RJ, UK
| | - David Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Johan Olofsson
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, SE-901 87, Sweden
| | - Matthias B Siewert
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, SE-901 87, Sweden
| | - Lorna E Street
- School of Geosciences, University of Edinburgh, Edinburgh,, EH9 3FF, UK
| | - Jens-Arne Subke
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Philip A Wookey
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
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16
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Abrego N, Huotari T, Tack AJM, Lindahl BD, Tikhonov G, Somervuo P, Martin Schmidt N, Ovaskainen O, Roslin T. Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient. Ecol Evol 2020; 10:8989-9002. [PMID: 32884673 PMCID: PMC7452766 DOI: 10.1002/ece3.6604] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/02/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022] Open
Abstract
How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
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Affiliation(s)
- Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Ayco J. M. Tack
- Department of EcologyEnvironment and Plant SciencesStockholm UniversityStockholmSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Gleb Tikhonov
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Computational Systems Biology groupDepartment of Computer ScienceAalto UniversityEspooFinland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | | | - Otso Ovaskainen
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
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17
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Abrego N, Roslin T, Huotari T, Tack AJM, Lindahl BD, Tikhonov G, Somervuo P, Schmidt NM, Ovaskainen O. Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities. Mol Ecol 2020; 29:2736-2746. [DOI: 10.1111/mec.15516] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Nerea Abrego
- Department of Agricultural Sciences University of Helsinki Helsinki Finland
| | - Tomas Roslin
- Department of Agricultural Sciences University of Helsinki Helsinki Finland
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tea Huotari
- Department of Agricultural Sciences University of Helsinki Helsinki Finland
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Uppsala Sweden
| | - Gleb Tikhonov
- Computational Systems Biology Group Department of Computer Science Aalto University Espoo Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
| | - Niels Martin Schmidt
- Arctic Research Centre Department of Bioscience Aarhus University Roskilde Denmark
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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Barbi F, Kohler A, Barry K, Baskaran P, Daum C, Fauchery L, Ihrmark K, Kuo A, LaButti K, Lipzen A, Morin E, Grigoriev IV, Henrissat B, Lindahl BD, Martin F. Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers. Environ Microbiol 2019; 22:1089-1103. [DOI: 10.1111/1462-2920.14873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/23/2019] [Accepted: 11/20/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Barbi
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014, SE‐750 07 Uppsala Sweden
| | - Annegret Kohler
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Preetisri Baskaran
- Department of Ecology Swedish University of Agricultural Sciences Box 7044, SE‐750 07 Uppsala Sweden
| | - Chris Daum
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Laure Fauchery
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Box 7026, 750 07 Uppsala Sweden
| | - Alan Kuo
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Emmanuelle Morin
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
- Department of Plant and Microbial Biology University of California, Berkeley Berkeley CA 94720 USA
| | - Bernard Henrissat
- CNRS UMR 7257, Aix‐Marseille University 13288 Marseille France
- INRA, USC 1408 AFMB 13288 Marseille France
- Department of Biological Sciences King Abdulaziz University Jeddah Saudi Arabia
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014, SE‐750 07 Uppsala Sweden
| | - Francis Martin
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry University 35 Qinghua East Road, Haidian Qu Beijing Shi 100083 China
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Zak DR, Pellitier PT, Argiroff W, Castillo B, James TY, Nave LE, Averill C, Beidler KV, Bhatnagar J, Blesh J, Classen AT, Craig M, Fernandez CW, Gundersen P, Johansen R, Koide RT, Lilleskov EA, Lindahl BD, Nadelhoffer KJ, Phillips RP, Tunlid A. Exploring the role of ectomycorrhizal fungi in soil carbon dynamics. New Phytol 2019; 223:33-39. [PMID: 30636276 DOI: 10.1111/nph.15679] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/07/2019] [Indexed: 05/26/2023]
Abstract
The extent to which ectomycorrhizal (ECM) fungi enable plants to access organic nitrogen (N) bound in soil organic matter (SOM) and transfer this growth-limiting nutrient to their plant host, has important implications for our understanding of plant-fungal interactions, and the cycling and storage of carbon (C) and N in terrestrial ecosystems. Empirical evidence currently supports a range of perspectives, suggesting that ECM vary in their ability to provide their host with N bound in SOM, and that this capacity can both positively and negatively influence soil C storage. To help resolve the multiplicity of observations, we gathered a group of researchers to explore the role of ECM fungi in soil C dynamics, and propose new directions that hold promise to resolve competing hypotheses and contrasting observations. In this Viewpoint, we summarize these deliberations and identify areas of inquiry that hold promise for increasing our understanding of these fundamental and widespread plant symbionts and their role in ecosystem-level biogeochemistry.
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Affiliation(s)
- Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter T Pellitier
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - WilliamA Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Buck Castillo
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Timothy Y James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lucas E Nave
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Colin Averill
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Kaitlyn V Beidler
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | | | - Jennifer Blesh
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aimée T Classen
- The Rubenstein School of Environment & Natural Resources, University of Vermont, Burlington, VT, 05405, USA
- The Gund Institute for Environment, University of Vermont, Burlington, VT, 05405, USA
| | - Matthew Craig
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | | | - Per Gundersen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, DK-1711, Denmark
| | - Renee Johansen
- Los Alamos National Laboratory, Santa Fe, NM, 87545, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Erik A Lilleskov
- US Forest Service, Northern Research Station, 410 Mac Innes Dr., Houghton, MI, 49931, USA
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Knute J Nadelhoffer
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Lund University, Lund, SE-221 00, Sweden
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Baskaran P, Ekblad A, Soucémarianadin LN, Hyvönen R, Schleucher J, Lindahl BD. Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species. FEMS Microbiol Ecol 2019; 95:5479879. [DOI: 10.1093/femsec/fiz059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/25/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
In boreal ecosystems plant production is often limited by low availability of nitrogen. Nitrogen retention in below-ground organic pools plays an important role in restricting recirculation to plants and thereby hampers forest production. Saprotrophic fungi are commonly assigned to different decomposer strategies, but how these relate to nitrogen cycling remains to be understood. Decomposition of Scots pine needle litter was studied in axenic microcosms with the ligninolytic litter decomposing basidiomycete Gymnopus androsaceus or the stress tolerant ascomycete Chalara longipes. Changes in chemical composition were followed by 13C CP/MAS NMR spectroscopy and nitrogen dynamics was assessed by the addition of a 15N tracer. Decomposition by C. longipes resulted in nitrogen retention in non-hydrolysable organic matter, enriched in aromatic and alkylic compounds, whereas the ligninolytic G. androsaceus was able to access this pool, counteracting nitrogen retention. Our observations suggest that differences in decomposing strategies between fungal species play an important role in regulating nitrogen retention and release during litter decomposition, implying that fungal community composition may impact nitrogen cycling at the ecosystem level.
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Affiliation(s)
- Preetisri Baskaran
- Swedish University of Agricultural Sciences, Department of Ecology, Box 7044, SE-750 07 Uppsala, Sweden
| | - Alf Ekblad
- Örebro University, School of Science and Technology, SE-70 182 Örebro, Sweden
| | - Laure N Soucémarianadin
- CNRS, Laboratoire de Géologie de l'ENS, Ecole Normale Supérieure, 75231 Paris, France
- Umeå University, Department of Medical Biochemistry and Biophysics, SE-901 87, Umeå, Sweden
| | - Riitta Hyvönen
- Swedish University of Agricultural Sciences, Department of Ecology, Box 7044, SE-750 07 Uppsala, Sweden
| | - Jürgen Schleucher
- Umeå University, Department of Medical Biochemistry and Biophysics, SE-901 87, Umeå, Sweden
| | - Björn D Lindahl
- Swedish University of Agricultural Sciences, Department of Soil and Environment, Box 7014, SE-750 07 Uppsala, Sweden
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21
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Sterkenburg E, Clemmensen KE, Lindahl BD, Dahlberg A. The significance of retention trees for survival of ectomycorrhizal fungi in clear‐cut Scots pine forests. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13363] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erica Sterkenburg
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences Uppsala Sweden
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences Uppsala Sweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural Sciences Uppsala Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences Uppsala Sweden
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22
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Kyaschenko J, Ovaskainen O, Ekblad A, Hagenbo A, Karltun E, Clemmensen KE, Lindahl BD. Soil fertility in boreal forest relates to root-driven nitrogen retention and carbon sequestration in the mor layer. New Phytol 2019; 221:1492-1502. [PMID: 30281792 DOI: 10.1111/nph.15454] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Boreal forest soils retain significant amounts of carbon (C) and nitrogen (N) in purely organic layers, but the regulation of organic matter turnover and the relative importance of leaf litter and root-derived inputs are not well understood. We combined bomb 14 C dating of organic matter with stable isotope profiling for Bayesian parameterization of an organic matter sequestration model. C and N dynamics were assessed across annual depth layers (cohorts), together representing 256 yr of organic matter accumulation. Results were related to ecosystem fertility (soil inorganic N, pH and litter C : N). Root-derived C was estimated to decompose two to 10 times more slowly than leaf litter, but more rapidly in fertile plots. The amounts of C and N per cohort declined during the initial 20 yr of decomposition, but, in older material, the amount of N per cohort increased, indicating N retention driven by root-derived C. The dynamics of root-derived inputs were more important than leaf litter dynamics in regulating the variation in organic matter accumulation along a forest fertility gradient. N retention in the rooting zone combined with impeded mining for N in less fertile ecosystems provides evidence for a positive feedback between ecosystem fertility and organic matter turnover.
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Affiliation(s)
- Julia Kyaschenko
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, FI-00014, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Alf Ekblad
- School of Science and Technology, Örebro University, SE-701 82, Örebro, Sweden
| | - Andreas Hagenbo
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Erik Karltun
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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23
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Rasmussen PU, Hugerth LW, Blanchet FG, Andersson AF, Lindahl BD, Tack AJM. Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb. New Phytol 2018; 220:1248-1261. [PMID: 29573431 PMCID: PMC6282561 DOI: 10.1111/nph.15088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/11/2018] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.
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Affiliation(s)
- Pil U. Rasmussen
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Luisa W. Hugerth
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
- Centre for Translational Microbiome ResearchDepartment of Molecular, Tumor and Cell BiologyScience for Life LaboratoryKarolinska Institutet171 65SolnaSweden
| | - F. Guillaume Blanchet
- Département de BiologieFaculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
| | - Anders F. Andersson
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
| | - Ayco J. M. Tack
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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24
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Castaño C, Lindahl BD, Alday JG, Hagenbo A, Martínez de Aragón J, Parladé J, Pera J, Bonet JA. Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest. New Phytol 2018; 220:1211-1221. [PMID: 29757469 DOI: 10.1111/nph.15205] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated the spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. Fungal communities in 336 soil samples collected monthly over 1 year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol. Community changes were analysed in the context of functional traits. Soil fungal biomass was lowest during summer and late winter and highest during autumn, concurrent with a greater relative abundance of mycorrhizal species. Intra-annual spatio-temporal changes in community composition correlated significantly with soil moisture and temperature. Mycorrhizal fungi were less affected by summer drought than free-living fungi. In particular, mycorrhizal species of the short-distance exploration type increased in relative abundance under dry conditions, whereas species of the long-distance exploration type were more abundant under wetter conditions. Our observations demonstrate a potential for compositional and functional shifts in fungal communities in response to changing climatic conditions. Free-living fungi and mycorrhizal species with extensive mycelia may be negatively affected by increasing drought periods in Mediterranean forest ecosystems.
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Affiliation(s)
- Carles Castaño
- Forest Bioengineering Solutions S.A., Crta. de Sant Llorenç de Morunys Km. 2, E-25280, Solsona, Spain
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
| | - Andreas Hagenbo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Juan Martínez de Aragón
- Forest Bioengineering Solutions S.A., Crta. de Sant Llorenç de Morunys Km. 2, E-25280, Solsona, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de St. Llorenç de Morunys km 2, E-25280, Solsona, Spain
| | - Javier Parladé
- Centre de Cabrils, IRTA, Ctra. Cabrils Km. 2, E-08348, Cabrils, Barcelona, Spain
| | - Joan Pera
- Centre de Cabrils, IRTA, Ctra. Cabrils Km. 2, E-08348, Cabrils, Barcelona, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de St. Llorenç de Morunys km 2, E-25280, Solsona, Spain
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25
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Sterkenburg E, Clemmensen KE, Ekblad A, Finlay RD, Lindahl BD. Contrasting effects of ectomycorrhizal fungi on early and late stage decomposition in a boreal forest. ISME J 2018; 12:2187-2197. [PMID: 29880913 PMCID: PMC6092328 DOI: 10.1038/s41396-018-0181-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/20/2018] [Accepted: 04/10/2018] [Indexed: 01/16/2023]
Abstract
Symbiotic ectomycorrhizal fungi have received increasing attention as regulators of below-ground organic matter storage. They are proposed to promote organic matter accumulation by suppressing saprotrophs, but have also been suggested to play an active role in decomposition themselves. Here we show that exclusion of tree roots and associated ectomycorrhizal fungi in a boreal forest increased decomposition of surface litter by 11% by alleviating nitrogen limitation of saprotrophs-a "Gadgil effect". At the same time, root exclusion decreased Mn-peroxidase activity in the deeper mor layer by 91%. Our results show that ectomycorrhizal fungi may hamper short-term litter decomposition, but also support a crucial role of ectomycorrhizal fungi in driving long-term organic matter oxidation. These observations stress the importance of ectomycorrhizal fungi in regulation of below-ground organic matter accumulation. By different mechanisms they may either hamper or stimulate decomposition, depending upon stage of decomposition and location in the soil profile.
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Affiliation(s)
- Erica Sterkenburg
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Box 7026, SE-750 07, Uppsala, Sweden
| | - Karina E Clemmensen
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Box 7026, SE-750 07, Uppsala, Sweden
| | - Alf Ekblad
- School of Science and Technology, Örebro University, SE-701 85, Örebro, Sweden
| | - Roger D Finlay
- Swedish University of Agricultural Sciences, Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Box 7026, SE-750 07, Uppsala, Sweden
| | - Björn D Lindahl
- Swedish University of Agricultural Sciences, Department of Soil and Environment, Box 7014, SE-750 07, Uppsala, Sweden.
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26
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Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytol 2018; 217:1213-1229. [PMID: 29315638 DOI: 10.1111/nph.14974] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/25/2017] [Indexed: 05/10/2023]
Abstract
Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.
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Affiliation(s)
- Elena Martino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Emmanuelle Morin
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Gwen-Aëlle Grelet
- Manaaki Whenua - Landcare Research, Ecosystems and Global Change Team, Gerald Street, PO Box 69040, Lincoln, 7640, New Zealand
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Annegret Kohler
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Nicolas Cichocki
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Rhyan B Dockter
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, 13288, France
| | - Rita C Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Erika A Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Jon Magnuson
- Pacific Northwest National Laboratory, Chemical and Biological Process Development Group, Richland, WA, 99354, USA
| | - Claude Murat
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Microbiology, Department of Biology, Utrecht University, 3508, TB Utrecht, the Netherlands
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Claire Veneault-Fourrey
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
- Laboratoire d'Excellence ARBRE, Faculté des Sciences et Technologies, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Université de Lorraine, Campus Aiguillettes, BP 70239, Vandoeuvre les Nancy cedex, 54506, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, 13288, France
- Department of Biological Sciences, King Abdulaziz University - KSA, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Francis M Martin
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280, Champenoux, France
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
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27
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Stendahl J, Berg B, Lindahl BD. Manganese availability is negatively associated with carbon storage in northern coniferous forest humus layers. Sci Rep 2017; 7:15487. [PMID: 29138466 PMCID: PMC5686207 DOI: 10.1038/s41598-017-15801-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 11/02/2017] [Indexed: 11/09/2022] Open
Abstract
Carbon sequestration below ground depends on organic matter input and decomposition, but regulatory bottlenecks remain unclear. The relative importance of plant production, climate and edaphic factors has to be elucidated to better predict carbon storage in forests. In Swedish forest soil inventory data from across the entire boreal latitudinal range (n = 2378), the concentration of exchangeable manganese was singled out as the strongest predictor (R2 = 0.26) of carbon storage in the extensive organic horizon (mor layer), which accounts for one third of the total below ground carbon. In comparison, established ecosystem models applied on the same data have failed to predict carbon stocks (R2 < 0.05), and in our study manganese availability overshadowed both litter production and climatic factors. We also identified exchangeable potassium as an additional strong predictor, however strongly correlated with manganese. The negative correlation between manganese and carbon highlights the importance of Mn-peroxidases in oxidative decomposition of recalcitrant organic matter. The results support the idea that the fungus-driven decomposition could be a critical factor regulating humus carbon accumulation in boreal forests, as Mn-peroxidases are specifically produced by basidiomycetes.
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Affiliation(s)
- Johan Stendahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7014, SE-75007, Uppsala, Sweden.
| | - Björn Berg
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7014, SE-75007, Uppsala, Sweden
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28
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Kyaschenko J, Clemmensen KE, Karltun E, Lindahl BD. Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities. Ecol Lett 2017; 20:1546-1555. [DOI: 10.1111/ele.12862] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/16/2017] [Accepted: 09/07/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Julia Kyaschenko
- Swedish University of Agricultural Sciences; Department of Soil and Environment; SE-750 07 Uppsala Sweden
| | - Karina E. Clemmensen
- Swedish University of Agricultural Sciences; Department of Forest Mycology and Plant Pathology; Uppsala BioCenter; SE-750 07 Uppsala Sweden
| | - Erik Karltun
- Swedish University of Agricultural Sciences; Department of Soil and Environment; SE-750 07 Uppsala Sweden
| | - Björn D. Lindahl
- Swedish University of Agricultural Sciences; Department of Soil and Environment; SE-750 07 Uppsala Sweden
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29
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Varenius K, Lindahl BD, Dahlberg A. Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests. FEMS Microbiol Ecol 2017; 93:4094915. [PMID: 28957584 DOI: 10.1093/femsec/fix105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/23/2017] [Indexed: 11/14/2022] Open
Abstract
Fennoscandian forestry has in the past decades changed from natural regeneration of forests towards replantation of clear-cuts, which negatively impacts ectomycorrhizal fungal (EMF) diversity. Retention of trees during harvesting enables EMF survival, and we therefore expected EMF communities to be more similar to those in old natural stands after forest regeneration using seed trees compared to full clear-cutting and replanting. We sequenced fungal internal transcribed spacer 2 (ITS2) amplicons to assess EMF communities in 10- to 60-year-old Scots pine stands regenerated either using seed trees or through replanting of clear-cuts with old natural stands as reference. We also investigated local EMF communities around retained old trees. We found that retention of seed trees failed to mitigate the impact of harvesting on EMF community composition and diversity. With increasing stand age, EMF communities became increasingly similar to those in old natural stands and permanently retained trees maintained EMF locally. From our observations, we conclude that EMF communities, at least common species, post-harvest are more influenced by environmental filtering, resulting from environmental changes induced by harvest, than by the continuity of trees. These results suggest that retention of intact forest patches is a more efficient way to conserve EMF diversity than retaining dispersed single trees.
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Affiliation(s)
- Kerstin Varenius
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7014, 750 07 Uppsala, Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
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30
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Manzoni S, Čapek P, Mooshammer M, Lindahl BD, Richter A, Šantrůčková H. Optimal metabolic regulation along resource stoichiometry gradients. Ecol Lett 2017; 20:1182-1191. [DOI: 10.1111/ele.12815] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/07/2017] [Accepted: 06/30/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research; Stockholm University; Stockholm Sweden
| | - Petr Čapek
- Department of Ecosystem Biology; University of South Bohemia; České Budějovice Czech Republic
| | - Maria Mooshammer
- Department of Microbiology and Ecosystem Science; University of Vienna; Vienna Austria
| | - Björn D. Lindahl
- Department of Soil and Environment; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science; University of Vienna; Vienna Austria
| | - Hana Šantrůčková
- Department of Ecosystem Biology; University of South Bohemia; České Budějovice Czech Republic
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Solly EF, Lindahl BD, Dawes MA, Peter M, Souza RC, Rixen C, Hagedorn F. Experimental soil warming shifts the fungal community composition at the alpine treeline. New Phytol 2017; 215:766-778. [PMID: 28543616 DOI: 10.1111/nph.14603] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Increased CO2 emissions and global warming may alter the composition of fungal communities through the removal of temperature limitation in the plant-soil system, faster nitrogen (N) cycling and changes in the carbon (C) allocation of host plants to the rhizosphere. At a Swiss treeline featuring Larix decidua and Pinus uncinata, the effects of multiple years of CO2 enrichment and experimental soil warming on the fungal community composition in the organic horizons were analysed using 454-pyrosequencing of ITS2 amplicons. Sporocarp production and colonization of ectomycorrhizal root tips were investigated in parallel. Fungal community composition was significantly altered by soil warming, whereas CO2 enrichment had little effect. Tree species influenced fungal community composition and the magnitude of the warming responses. The abundance of ectomycorrhizal fungal taxa was positively correlated with N availability, and ectomycorrhizal taxa specialized for conditions of high N availability proliferated with warming, corresponding to considerable increases in inorganic N in warmed soils. Traits related to N utilization are important in determining the responses of ectomycorrhizal fungi to warming in N-poor cold ecosystems. Shifts in the overall fungal community composition in response to higher temperatures may alter fungal-driven processes with potential feedbacks on ecosystem N cycling and C storage at the alpine treeline.
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Affiliation(s)
- Emily F Solly
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 75007, Uppsala, Sweden
| | - Melissa A Dawes
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Martina Peter
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Rômulo C Souza
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Christian Rixen
- WSL Institute for Snow and Avalanche Research (SLF), Flüelastrasse 11, 7260, Davos, Switzerland
| | - Frank Hagedorn
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
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33
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Kyaschenko J, Clemmensen KE, Hagenbo A, Karltun E, Lindahl BD. Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands. ISME J 2017; 11:863-874. [PMID: 28085155 PMCID: PMC5364365 DOI: 10.1038/ismej.2016.184] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/06/2016] [Accepted: 11/07/2016] [Indexed: 11/08/2022]
Abstract
Forestry reshapes ecosystems with respect to tree age structure, soil properties and vegetation composition. These changes are likely to be paralleled by shifts in microbial community composition with potential feedbacks on ecosystem functioning. Here, we assessed fungal communities across a chronosequence of managed Pinus sylvestris stands and investigated correlations between taxonomic composition and extracellular enzyme activities. Not surprisingly, clear-cutting had a negative effect on ectomycorrhizal fungal abundance and diversity. In contrast, clear-cutting favoured proliferation of saprotrophic fungi correlated with enzymes involved in holocellulose decomposition. During stand development, the re-establishing ectomycorrhizal fungal community shifted in composition from dominance by Atheliaceae in younger stands to Cortinarius and Russula species in older stands. Late successional ectomycorrhizal taxa correlated with enzymes involved in mobilisation of nutrients from organic matter, indicating intensified nutrient limitation. Our results suggest that maintenance of functional diversity in the ectomycorrhizal fungal community may sustain long-term forest production by retaining a capacity for symbiosis-driven recycling of organic nutrient pools.
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Affiliation(s)
- Julia Kyaschenko
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andreas Hagenbo
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Karltun
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Hagenbo A, Clemmensen KE, Finlay RD, Kyaschenko J, Lindahl BD, Fransson P, Ekblad A. Changes in turnover rather than production regulate biomass of ectomycorrhizal fungal mycelium across a Pinus sylvestris chronosequence. New Phytol 2017; 214:424-431. [PMID: 27997034 DOI: 10.1111/nph.14379] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
In boreal forest soils, ectomycorrhizal fungi are fundamentally important for carbon (C) dynamics and nutrient cycling. Although their extraradical mycelium (ERM) is pivotal for processes such as soil organic matter build-up and nitrogen cycling, very little is known about its dynamics and regulation. In this study, we quantified ERM production and turnover, and examined how these two processes together regulated standing ERM biomass in seven sites forming a chronosequence of 12- to 100-yr-old managed Pinus sylvestris forests. This was done by determining ERM biomass, using ergosterol as a proxy, in sequentially harvested in-growth mesh bags and by applying mathematical models. Although ERM production declined with increasing forest age from 1.2 to 0.5 kg ha-1 d-1 , the standing biomass increased from 50 to 112 kg ha-1 . This was explained by a drastic decline in mycelial turnover from seven times to one time per year with increasing forest age, corresponding to mean residence times from 25 d up to 1 yr. Our results demonstrate that ERM turnover is the main factor regulating biomass across differently aged forest stands. Explicit inclusion of ERM parameters in forest ecosystem C models may significantly improve their capacity to predict responses of mycorrhiza-mediated processes to management and environmental changes.
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Affiliation(s)
- Andreas Hagenbo
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Julia Kyaschenko
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Petra Fransson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Alf Ekblad
- School of Science and Technology, Örebro University, Örebro, SE-701 82, Sweden
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Baskaran P, Hyvönen R, Berglund SL, Clemmensen KE, Ågren GI, Lindahl BD, Manzoni S. Modelling the influence of ectomycorrhizal decomposition on plant nutrition and soil carbon sequestration in boreal forest ecosystems. New Phytol 2017; 213:1452-1465. [PMID: 27748949 DOI: 10.1111/nph.14213] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/15/2016] [Indexed: 05/26/2023]
Abstract
Tree growth in boreal forests is limited by nitrogen (N) availability. Most boreal forest trees form symbiotic associations with ectomycorrhizal (ECM) fungi, which improve the uptake of inorganic N and also have the capacity to decompose soil organic matter (SOM) and to mobilize organic N ('ECM decomposition'). To study the effects of 'ECM decomposition' on ecosystem carbon (C) and N balances, we performed a sensitivity analysis on a model of C and N flows between plants, SOM, saprotrophs, ECM fungi, and inorganic N stores. The analysis indicates that C and N balances were sensitive to model parameters regulating ECM biomass and decomposition. Under low N availability, the optimal C allocation to ECM fungi, above which the symbiosis switches from mutualism to parasitism, increases with increasing relative involvement of ECM fungi in SOM decomposition. Under low N conditions, increased ECM organic N mining promotes tree growth but decreases soil C storage, leading to a negative correlation between C stores above- and below-ground. The interplay between plant production and soil C storage is sensitive to the partitioning of decomposition between ECM fungi and saprotrophs. Better understanding of interactions between functional guilds of soil fungi may significantly improve predictions of ecosystem responses to environmental change.
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Affiliation(s)
- Preetisri Baskaran
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, SE-750 07, Sweden
| | - Riitta Hyvönen
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, SE-750 07, Sweden
| | - S Linnea Berglund
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, SE-750 07, Sweden
| | - Karina E Clemmensen
- Department of Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Göran I Ågren
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, SE-750 07, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, Uppsala, SE-750 07, Sweden
| | - Stefano Manzoni
- Department of Physical Geography, Stockholm University, Stockholm, SE-106 91, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, SE-106 91, Sweden
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Jonsson M, Snäll T, Asplund J, Clemmensen KE, Dahlberg A, Kumordzi BB, Lindahl BD, Oksanen J, Wardle DA. Divergent responses of β‐diversity among organism groups to a strong environmental gradient. Ecosphere 2016. [DOI: 10.1002/ecs2.1535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Micael Jonsson
- Department of Ecology and Environmental Science Umeå University SE‐901 87 Umeå Sweden
| | - Tord Snäll
- Swedish Species Information Centre Swedish University of Agricultural Sciences Box 7007 SE‐750 07 Uppsala Sweden
| | - Johan Asplund
- Department of Ecology and Natural Resource Management Norwegian University of Life Sciences NO‐1432 Aas Norway
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Box 7026 SE‐750 07 Uppsala Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Box 7026 SE‐750 07 Uppsala Sweden
| | - Bright B. Kumordzi
- Department of Forest Ecology and Management Swedish University of Agricultural Sciences SE‐90183 Umeå Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014 SE‐75007 Uppsala Sweden
| | - Jari Oksanen
- Department of Ecology University of Oulu FI‐90014 Oulu Finland
| | - David A. Wardle
- Department of Forest Ecology and Management Swedish University of Agricultural Sciences SE‐90183 Umeå Sweden
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Bödeker ITM, Lindahl BD, Olson Å, Clemmensen KE. Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12677] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Inga T. M. Bödeker
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
- Southern Swedish Forest Research Centre Swedish University of Agricultural Sciences Box 49 SE‐230 53 Alnarp Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014 SE‐750 07 Uppsala Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
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Abstract
Fungal species participate in vast numbers of processes in the landscape around us. However, their often cryptic growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Recent technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enable identification and relative quantification of fungal community members across well-replicated experimental settings. Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, that is, the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon mix to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.
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Affiliation(s)
- Karina Engelbrecht Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 7026, SE-750 07, Uppsala, Sweden.
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 7026, SE-750 07, Uppsala, Sweden.
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 7026, SE-750 07, Uppsala, Sweden.
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 7014, SE-750 07, Uppsala, Sweden.
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Hiscox J, Savoury M, Müller CT, Lindahl BD, Rogers HJ, Boddy L. Priority effects during fungal community establishment in beech wood. ISME J 2015; 9:2246-60. [PMID: 25798754 PMCID: PMC4579477 DOI: 10.1038/ismej.2015.38] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/28/2015] [Accepted: 02/06/2015] [Indexed: 11/13/2022]
Abstract
Assembly history of fungal communities has a crucial role in the decomposition of woody resources, and hence nutrient cycling and ecosystem function. However, it has not been clearly determined whether the fungal species that arrive first may, potentially, dictate the subsequent pathway of community development, that is, whether there is a priority effect at the species level. We used traditional culture-based techniques coupled with sequencing of amplified genetic markers to profile the fungal communities in beech (Fagus sylvatica) disks that had been pre-colonised separately with nine species from various stages of fungal succession. Clear differences in community composition were evident following pre-colonisation by different species with three distinct successor communities identified, indicating that individual species may have pivotal effects in driving assembly history. Priority effects may be linked to biochemical alteration of the resource and combative ability of the predecessor.
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Affiliation(s)
- Jennifer Hiscox
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Melanie Savoury
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff CF10 3AX, UK
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Sterkenburg E, Bahr A, Brandström Durling M, Clemmensen KE, Lindahl BD. Changes in fungal communities along a boreal forest soil fertility gradient. New Phytol 2015; 207:1145-58. [PMID: 25952659 DOI: 10.1111/nph.13426] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/19/2015] [Indexed: 05/21/2023]
Abstract
Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests.
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Affiliation(s)
- Erica Sterkenburg
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Adam Bahr
- Microbial Ecology, Department of Biology, Lund University, Lund, SE-223 62, Sweden
| | - Mikael Brandström Durling
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Karina E Clemmensen
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, Uppsala, SE-750 07, Sweden
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Lindahl BD, Tunlid A. Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs. New Phytol 2015; 205:1443-1447. [PMID: 25524234 DOI: 10.1111/nph.13201] [Citation(s) in RCA: 305] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/23/2014] [Indexed: 05/18/2023]
Abstract
Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by 'brown-rot' Fenton chemistry or using 'white-rot' peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes.
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Affiliation(s)
- Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-750 07, Uppsala, Sweden
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, SE-22 362, Lund, Sweden
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Clemmensen KE, Finlay RD, Dahlberg A, Stenlid J, Wardle DA, Lindahl BD. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. New Phytol 2015; 205:1525-1536. [PMID: 25494880 DOI: 10.1111/nph.13208] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/05/2014] [Indexed: 05/15/2023]
Abstract
Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems. We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration. In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition. Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests.
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Affiliation(s)
- Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - David A Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-75007, Uppsala, Sweden
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43
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Affiliation(s)
- David A Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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Bödeker ITM, Clemmensen KE, de Boer W, Martin F, Olson Å, Lindahl BD. Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems. New Phytol 2014; 203:245-56. [PMID: 24725281 DOI: 10.1111/nph.12791] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/28/2014] [Indexed: 05/22/2023]
Abstract
In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N. In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed. We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases - a number comparable to many white-rot wood decomposers. These results support the hypothesis that some ectomycorrhizal fungi--Cortinarius species in particular--may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.
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Affiliation(s)
- Inga T M Bödeker
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden; Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 49, 230 53, Alnarp, Sweden
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Nilsson RH, Hyde KD, Pawłowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl BD, Lindner D, Liu JK, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sánchez-García M, de Sousa F, Stefańczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson KH, Kõljalg U, Abarenkov K. Improving ITS sequence data for identification of plant pathogenic fungi. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0291-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Boberg JB, Finlay RD, Stenlid J, Ekblad A, Lindahl BD. Nitrogen and carbon reallocation in fungal mycelia during decomposition of boreal forest litter. PLoS One 2014; 9:e92897. [PMID: 24651625 PMCID: PMC3961408 DOI: 10.1371/journal.pone.0092897] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/26/2014] [Indexed: 11/25/2022] Open
Abstract
Boreal forests are characterized by spatially heterogeneous soils with low N availability. The decomposition of coniferous litter in these systems is primarily performed by basidiomycete fungi, which often form large mycelia with a well-developed capacity to reallocate resources spatially- an advantageous trait in heterogeneous environments. In axenic microcosm systems we tested whether fungi increase their biomass production by reallocating N between Pinus sylvestris (Scots pine) needles at different stages of decomposition. We estimated fungal biomass production by analysing the accumulation of the fungal cell wall compound chitin. Monospecific systems were compared with systems with interspecific interactions. We found that the fungi reallocated assimilated N and mycelial growth away from well-degraded litter towards fresh litter components. This redistribution was accompanied by reduced decomposition of older litter. Interconnection of substrates increased over-all fungal C use efficiency (i.e. the allocation of assimilated C to biomass rather than respiration), presumably by enabling fungal translocation of growth-limiting N to litter with higher C quality. Fungal connection between different substrates also restricted N-mineralization and production of dissolved organic N, suggesting that litter saprotrophs in boreal forest ecosystems primarily act to redistribute rather than release N. This spatial integration of different resource qualities was hindered by interspecific interactions, in which litters of contrasting quality were colonised by two different basidiomycete species. The experiments provide a detailed picture of how resource reallocation in two decomposer fungi leads to a more efficient utilisation of spatially separated resources under N-limitation. From an ecosystem point of view, such economic fungal behaviour could potentially contribute to organic matter accumulation in the litter layers of boreal forests.
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Affiliation(s)
- Johanna B. Boberg
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger D. Finlay
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Stenlid
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alf Ekblad
- Örebro Isotope Laboratory, School of Science and Technology, Bilberg Building, Örebro University, Örebro, Sweden
| | - Björn D. Lindahl
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 2013; 22:5271-5277. [PMID: 24112409 DOI: 10.1111/j.1365-2745.2011.01940.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/08/2013] [Accepted: 07/17/2013] [Indexed: 05/20/2023]
Abstract
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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Affiliation(s)
- Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
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48
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Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 2013; 22:5271-7. [DOI: 10.1111/mec.12481] [Citation(s) in RCA: 2233] [Impact Index Per Article: 203.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/08/2013] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
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49
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Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide. New Phytol 2013; 199:288-299. [PMID: 23534863 PMCID: PMC3712477 DOI: 10.1111/nph.12243] [Citation(s) in RCA: 510] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/18/2013] [Indexed: 05/17/2023]
Abstract
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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Affiliation(s)
- Björn D Lindahl
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Tor Carlsen
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Taina Pennanen
- The Finnish Forest Research Institute, PL 18, FI-01301, Vantaa, Finland
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Håvard Kauserud
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
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Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, Strid Y, Stenlid J, Brandström-Durling M, Clemmensen KE, Lindahl BD. New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 2012; 82:666-77. [PMID: 22738186 DOI: 10.1111/j.1574-6941.2012.01437.x] [Citation(s) in RCA: 947] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/15/2012] [Accepted: 06/22/2012] [Indexed: 01/09/2023] Open
Abstract
With recent methodological advances, molecular markers are increasingly used for semi-quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes through PCR places new demands on primers to accurately match target sites and provide short amplicons. The internal transcribed spacer (ITS) region of the ribosome encoding genes is a commonly used marker for many fungal groups. Here, we describe three new primers - fITS7, gITS7 and fITS9, which may be used to amplify the fungal ITS2 region by targeting sites in the 5.8S encoding gene. We evaluated the primers and compared their performance with the commonly used ITS1f primer by 454-sequencing of both artificially assembled templates and field samples. When the entire ITS region was amplified using the ITS1f/ITS4 primer combination, we found strong bias against species with longer amplicons. This problem could be overcome by using the new primers, which produce shorter amplicons and better preserve the quantitative composition of the template. In addition, the new primers yielded more diverse amplicon communities than the ITS1f primer.
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Affiliation(s)
- Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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