1
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Nelson AR, Fegel TS, Danczak RE, Caiafa MV, Roth HK, Dunn OI, Turvold CA, Borch T, Glassman SI, Barnes RT, Rhoades CC, Wilkins MJ. Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. ISME J 2024; 18:wrae047. [PMID: 38502869 DOI: 10.1093/ismejo/wrae047] [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: 11/07/2023] [Revised: 01/12/2024] [Accepted: 03/17/2024] [Indexed: 03/21/2024]
Abstract
Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, US Forest Service, Fort Collins, CO 80526, United States
| | - Robert E Danczak
- Division of Biological Sciences, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Marcos V Caiafa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States
| | - Oliver I Dunn
- The Environmental Studies Program, Colorado College, Colorado Springs, CO 80946, United States
| | - Cosette A Turvold
- The Environmental Studies Program, Colorado College, Colorado Springs, CO 80946, United States
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, United States
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Rebecca T Barnes
- The Environmental Studies Program, Colorado College, Colorado Springs, CO 80946, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, US Forest Service, Fort Collins, CO 80526, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
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2
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Krichels AH, Greene AC, Jenerette GD, Spasojevic MJ, Glassman SI, Homyak PM. Precipitation legacies amplify ecosystem nitrogen losses from nitric oxide emissions in a Pinyon-Juniper dryland. Ecology 2023; 104:e3930. [PMID: 36451599 DOI: 10.1002/ecy.3930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/04/2022]
Abstract
Climate change is increasing the variability of precipitation, altering the frequency of soil drying-wetting events and the distribution of seasonal precipitation. These changes in precipitation can alter nitrogen (N) cycling and stimulate nitric oxide (NO) emissions (an air pollutant at high concentrations), which may vary according to legacies of past precipitation and represent a pathway for ecosystem N loss. To identify whether precipitation legacies affect NO emissions, we excluded or added precipitation during the winter growing season in a Pinyon-Juniper dryland and measured in situ NO emissions following experimental wetting. We found that the legacy of both excluding and adding winter precipitation increased NO emissions early in the following summer; cumulative NO emissions from the winter precipitation exclusion plots (2750 ± 972 μg N-NO m-2 ) and winter water addition plots (2449 ± 408 μg N-NO m-2 ) were higher than control plots (1506 ± 397 μg N-NO m-2 ). The increase in NO emissions with previous precipitation exclusion was associated with inorganic N accumulation, while the increase in NO emissions with previous water addition was associated with an upward trend in microbial biomass. Precipitation legacies can accelerate soil NO emissions and may amplify ecosystem N loss in response to more variable precipitation.
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Affiliation(s)
- Alexander H Krichels
- Environmental Sciences, University of California, Riverside, California, USA.,Center for Conservation Biology, University of California, Riverside, California, USA
| | - Aral C Greene
- Environmental Sciences, University of California, Riverside, California, USA
| | - G Darrel Jenerette
- Center for Conservation Biology, University of California, Riverside, California, USA.,Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Marko J Spasojevic
- Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
| | - Sydney I Glassman
- Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Peter M Homyak
- Environmental Sciences, University of California, Riverside, California, USA.,Center for Conservation Biology, University of California, Riverside, California, USA
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3
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Pulido-Chavez MF, Randolph JWJ, Zalman C, Larios L, Homyak PM, Glassman SI. Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire. Mol Ecol 2022; 32:1685-1707. [PMID: 36579900 DOI: 10.1111/mec.16835] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/30/2022]
Abstract
The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.
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Affiliation(s)
- M Fabiola Pulido-Chavez
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
| | - James W J Randolph
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
| | - Cassandra Zalman
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Loralee Larios
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, USA
| | - Peter M Homyak
- Department of Environmental Sciences, University of California-Riverside, Riverside, California, USA
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
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4
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Fox S, Sikes BA, Brown SP, Cripps CL, Glassman SI, Hughes K, Semenova-Nelsen T, Jumpponen A. Fire as a driver of fungal diversity - A synthesis of current knowledge. Mycologia 2022; 114:215-241. [PMID: 35344467 DOI: 10.1080/00275514.2021.2024422] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or "fire-loving," fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.
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Affiliation(s)
- Sam Fox
- Division of Biology, Kansas State University, Manhattan, Kansas 66506.,Department of Natural Resources and Society, University of Idaho, Moscow, Idaho 83844
| | - Benjamin A Sikes
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Shawn P Brown
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152
| | - Cathy L Cripps
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Sydney I Glassman
- Department of Microbiology & Plant Pathology, University of California at Riverside, Riverside, California 92521
| | - Karen Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37996
| | - Tatiana Semenova-Nelsen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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5
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Enright DJ, Frangioso KM, Isobe K, Rizzo DM, Glassman SI. Mega‐fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. Mol Ecol 2022; 31:2475-2493. [DOI: 10.1111/mec.16399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Dylan J. Enright
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
| | - Kerri M. Frangioso
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Kazuo Isobe
- Department of Applied Biological Chemistry Graduate School of Agricultural and Life Sciences The University of Tokyo 1‐1‐1 Yayoi, Bunkyo‐ku Tokyo 113‐8657
| | - David M. Rizzo
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Sydney I. Glassman
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
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6
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Gill NS, Turner MG, Brown CD, Glassman SI, Haire SL, Hansen WD, Pansing ER, St Clair SB, Tomback DF. Limitations to Propagule Dispersal Will Constrain Postfire Recovery of Plants and Fungi in Western Coniferous Forests. Bioscience 2022. [DOI: 10.1093/biosci/biab139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Many forest species are adapted to long-interval, high-severity fires, but the intervals between severe fires are decreasing with changes in climate, land use, and biological invasions. Although the effects of changing fire regimes on some important recovery processes have previously been considered, the consequences for the dispersal of propagules (plant seeds and fungal spores) in forest communities have not. We characterize three mechanisms by which changing fire regimes disrupt propagule dispersal in mesic temperate, boreal, and high-elevation forests: reduced abundance and altered spatial distributions of propagule source populations, less effective dispersal of propagules by wind, and altered behavior of animal dispersers and propagule predators. We consider how disruptions to propagule dispersal may interact with other factors that are also influenced by fire regime change, potentially increasing risk of forest conversion. Finally, we highlight urgent research topics regarding how dispersal limitation may shape twenty-first century forest recovery after stand-replacing fire.
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Affiliation(s)
- Nathan S Gill
- Texas Tech University, Lubbock, Texas, United States
| | - Monica G Turner
- University of Wisconsin–Madison, Madison, Wisconsin, United States
| | - Carissa D Brown
- Memorial University, St. John's, Newfoundland and Labrador, Canada
| | | | - Sandra L Haire
- Haire Laboratory for Landscape Ecology, Tucson, Arizona, United States
| | | | | | | | - Diana F Tomback
- University of Colorado Denver, Denver, Colorado, United States
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7
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Alster CJ, Allison SD, Johnson NG, Glassman SI, Treseder KK. Phenotypic plasticity of fungal traits in response to moisture and temperature. ISME Commun 2021; 1:43. [PMID: 36740602 PMCID: PMC9723763 DOI: 10.1038/s43705-021-00045-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4-50% water holding capacity) and at five temperatures (ranging from 4-36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
- School of Science, University of Waikato, Hamilton, New Zealand.
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Nels G Johnson
- USDA Forest Service, Pacific Southwest Research Station, Albany, CA, USA
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
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8
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Davison J, Moora M, Semchenko M, Adenan SB, Ahmed T, Akhmetzhanova AA, Alatalo JM, Al-Quraishy S, Andriyanova E, Anslan S, Bahram M, Batbaatar A, Brown C, Bueno CG, Cahill J, Cantero JJ, Casper BB, Cherosov M, Chideh S, Coelho AP, Coghill M, Decocq G, Dudov S, Fabiano EC, Fedosov VE, Fraser L, Glassman SI, Helm A, Henry HAL, Hérault B, Hiiesalu I, Hiiesalu I, Hozzein WN, Kohout P, Kõljalg U, Koorem K, Laanisto L, Mander Ü, Mucina L, Munyampundu JP, Neuenkamp L, Niinemets Ü, Nyamukondiwa C, Oja J, Onipchenko V, Pärtel M, Phosri C, Põlme S, Püssa K, Ronk A, Saitta A, Semboli O, Sepp SK, Seregin A, Sudheer S, Peña-Venegas CP, Paz C, Vahter T, Vasar M, Veraart AJ, Tedersoo L, Zobel M, Öpik M. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. New Phytol 2021; 231:763-776. [PMID: 33507570 DOI: 10.1111/nph.17240] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 09/08/2020] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- School of Earth and Environmental Sciences, University of Manchester, Manchester,, M13 9PL, UK
| | | | - Talaat Ahmed
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Asem A Akhmetzhanova
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Juha M Alatalo
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Elena Andriyanova
- Institute of Biological Problems of the North Far East Branch of Russian Academy of Sciences, Magadan, 685000, Russia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 756 51, Sweden
| | - Amgaa Batbaatar
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, X5000HUA, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Brenda B Casper
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Mikhail Cherosov
- Institute of Biological Problems of the Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, 677000, Russia
| | - Saida Chideh
- Département de Recherche en Sciences de l'Environnement, Université de Djibouti, Private bag 1904, Djibouti, Djibouti
| | - Ana P Coelho
- Department of Biology and CESAM, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Matthew Coghill
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, F-80037, France
| | - Sergey Dudov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Ezequiel Chimbioputo Fabiano
- Department of Wildlife Management and Ecotourism, University of Namibia, Private bag 1096, Katima Mulilo, Namibia
| | - Vladimir E Fedosov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
- Botanical Garden-Institute FEB RAS, Vladivostok, 690024, Russia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bruno Hérault
- CIRAD, UPR Forêts et Sociétés, Yamoussoukro, Côte d'Ivoire
- Forêts et Sociétés, Université de Montpellier, CIRAD, Montpellier, 34000, France
- Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro, Côte d'Ivoire
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Bani Suwayf, 62511, Egypt
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Science, Prague, 14220, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 12843, Czechia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, WA, 6150, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, Kigali, 3900, Rwanda
| | - Lena Neuenkamp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Institute of Plant Sciences, University of Bern, Bern, 3013, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private bag 16, Palapye, Botswana
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Sergei Põlme
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Natural History Museum, University of Tartu, Tartu, 51014, Estonia
| | - Kersti Püssa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Argo Ronk
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, 90128, Italy
| | - Olivia Semboli
- Center of Studies and Research on Pharmacopoeia and Traditional African Medicine, University of Bangui, Bangui, Central African Republic
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Alexey Seregin
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Surya Sudheer
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Clara P Peña-Venegas
- Instituto Amazónico de Investigaciones Científicas Sinchi, Leticia, Amazonas, 910001, Colombia
| | - Claudia Paz
- Departamento de Biodiversidade, Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, 6525AJ, the Netherlands
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, 51005, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
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9
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Alster CJ, Allison SD, Glassman SI, Martiny AC, Treseder KK. Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland. Front Microbiol 2021; 12:655987. [PMID: 33995318 PMCID: PMC8118720 DOI: 10.3389/fmicb.2021.655987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States
| | - Adam C Martiny
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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10
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Livne-Luzon S, Shemesh H, Osem Y, Carmel Y, Migael H, Avidan Y, Tsafrir A, Glassman SI, Bruns TD, Ovadia O. High resilience of the mycorrhizal community to prescribed seasonal burnings in eastern Mediterranean woodlands. Mycorrhiza 2021; 31:203-216. [PMID: 33475801 DOI: 10.1007/s00572-020-01010-5] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Fire effects on ecosystems range from destruction of aboveground vegetation to direct and indirect effects on belowground microorganisms. Although variation in such effects is expected to be related to fire severity, another potentially important and poorly understood factor is the effect of fire seasonality on soil microorganisms. We carried out a large-scale field experiment examining the effects of spring (early-dry season) versus autumn (late-dry- season) burns on the community composition of soil fungi in a typical Mediterranean woodland. Although the intensity and severity of our prescribed burns were largely consistent between the two burning seasons, we detected differential fire season effects on the composition of the soil fungal community, driven by changes in the saprotrophic fungal guild. The community composition of ectomycorrhizal fungi, assayed both in pine seedling bioassays and from soil sequencing, appeared to be resilient to the variation inflicted by seasonal fires. Since changes in the soil saprotrophic fungal community can directly influence carbon emission and decomposition rates, we suggest that regardless of their intensity and severity, seasonal fires may cause changes in ecosystem functioning.
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Affiliation(s)
- Stav Livne-Luzon
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel.
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Hagai Shemesh
- Department of Environmental Sciences, Tel-Hai College, Kiryat Shmona, 1220800, Israel
| | - Yagil Osem
- Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Bet Dagan, Israel
| | - Yohay Carmel
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hen Migael
- Department of Environmental Sciences, Tel-Hai College, Kiryat Shmona, 1220800, Israel
| | - Yael Avidan
- Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Sede Boqer Campus, 84990, Israel
| | - Anat Tsafrir
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, UC Riverside, Riverside, CA, 92521, USA
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, 94720-3102, USA
| | - Ofer Ovadia
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel.
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11
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Livne-Luzon S, Shemesh H, Osem Y, Carmel Y, Migael H, Avidan Y, Tsafrir A, Glassman SI, Bruns TD, Ovadia O. Correction to: High resilience of the mycorrhizal community to prescribed seasonal burnings in eastern Mediterranean woodlands. Mycorrhiza 2021; 31:217. [PMID: 33619656 DOI: 10.1007/s00572-021-01022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Stav Livne-Luzon
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel.
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Hagai Shemesh
- Department of Environmental Sciences, Tel-Hai College, Kiryat Shmona, 1220800, Israel
| | - Yagil Osem
- Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Bet Dagan, Israel
| | - Yohay Carmel
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hen Migael
- Department of Environmental Sciences, Tel-Hai College, Kiryat Shmona, 1220800, Israel
| | - Yael Avidan
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Anat Tsafrir
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, UC Riverside, Riverside, CA, 92521, USA
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, 94720-3102, USA
| | - Ofer Ovadia
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer Sheva, 84105, Israel.
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12
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Carey CJ, Glassman SI, Bruns TD, Aronson EL, Hart SC. Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms? Ecol Evol 2020; 10:6593-6609. [PMID: 32724535 PMCID: PMC7381575 DOI: 10.1002/ece3.6392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/20/2020] [Revised: 03/29/2020] [Accepted: 04/22/2020] [Indexed: 02/01/2023] Open
Abstract
Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next-generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0-5 cm) beneath giant sequoia and co-occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove-dependent.
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Affiliation(s)
| | - Sydney I. Glassman
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Thomas D. Bruns
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Emma L. Aronson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Stephen C. Hart
- Department of Life and Environmental Sciences and the Sierra Nevada Research InstituteUniversity of CaliforniaMercedCAUSA
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13
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Bruns TD, Chung JA, Carver AA, Glassman SI. A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species. PLoS One 2020; 15:e0222691. [PMID: 32130222 PMCID: PMC7055920 DOI: 10.1371/journal.pone.0222691] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/14/2020] [Indexed: 01/06/2023] Open
Abstract
We have designed a pyrocosm to enable fine-scale dissection of post-fire soil microbial communities. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near this peak for a significant time, and is accurately predicted by soil depth and the mass of charcoal burned. Flash fuels that produce no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of pyrophilous fungus, within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change noticeably with the fire, although there is an overall reduction in richness and evenness. We introduce a thermo-chemical gradient model to summarize the way that heat, soil depth and altered soil chemistry interact to create a predictable, depth-structured habitat for microbes in post-fire soils. Coupling this model with the temperature relationships found in the pyrocosms, we predict that the width of a survivable “goldilocks zone”, which achieves temperatures that select for postfire-adapted microbes, will stay relatively constant across a range of fuel loads. In addition we predict that a larger necromass zone, containing labile carbon and nutrients from recently heat-killed organisms, will increase in size rapidly with addition of fuel and then remain nearly constant in size over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.
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Affiliation(s)
- Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
| | - Judy A. Chung
- Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, California, United States of America
| | - Akiko A. Carver
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Sydney I. Glassman
- Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, California, United States of America
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14
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Nilsson RH, Taylor AFS, Adams RI, Baschien C, Johan Bengtsson-Palme, Cangren P, Coleine C, Heide-Marie Daniel, Glassman SI, Hirooka Y, Irinyi L, Reda Iršėnaitė, Pedro M. Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M. Visagie, Weiss M, Woudenberg JHC, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K. Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys 2018; 28:65-82. [PMID: 29559822 PMCID: PMC5804120 DOI: 10.3897/mycokeys.28.20887] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 09/09/2017] [Accepted: 11/12/2017] [Indexed: 12/22/2022] Open
Abstract
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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Affiliation(s)
- R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Andy F. S. Taylor
- The James Hutton Institute and University of Aberdeen, Aberdeen, United Kingdom
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, 94720 Berkeley, California, USA
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
- Department of Plant Pathology & Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, Riverside 92501, CA, USA
| | - Heide-Marie Daniel
- Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, BCCM/MUCL, Louvain-la-Neuve, Belgium
| | - Sydney I. Glassman
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo Japan 184-8584
| | - Laszlo Irinyi
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Reda Iršėnaitė
- Institute of Botany, Nature Research Centre, Žaliųjų ežerų Str. 49, 08406 Vilnius, Lithuania
| | - Pedro M. Martin-Sanchez
- Bundesanstalt für Materialforschung und -prüfung (BAM), Department 4. Materials & Environment, Unter den Eichen 87, 12205 Berlin, Germany
| | - Wieland Meyer
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jose Paulo Sampaio
- UCIBIO-REQUIMTE, DCV, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Frantisek Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i, Prague, Czech Republic
| | - Dirk Stubbe
- BCCM/IHEM, Scientific Institute of Public Health WIV-ISP, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Sung-Oui Suh
- ATCC, 10801 University Blvd., Manassas, Virginia 20110, USA
| | - Richard Summerbell
- Sporometrics, 219 Dufferin Street, Suite 20C, Toronto, Ontario Canada, M6K 1Y9
- Dalla Lana School of Public Health, University of Toronto, Health Sciences Building, 155 College Street, 6th floor, Toronto, Ontario Canada, M5T 3M7
| | - Sten Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Martin Unterseher
- Evangelisches Schulzentrum Martinschule, Max-Planck-Str. 7, 17491 Greifswald, Germany
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
| | - Michael Weiss
- Steinbeis-Innovationszentrum, Organismische Mykologie und Mikrobiologie, Vor dem Kreuzberg 17, 72070 Tübingen, Germany
| | - Joyce HC Woudenberg
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
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15
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Glassman SI, Wang IJ, Bruns TD. Environmental filtering by
pH
and soil nutrients drives community assembly in fungi at fine spatial scales. Mol Ecol 2017; 26:6960-6973. [DOI: 10.1111/mec.14414] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Sydney I. Glassman
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology University of California, Irvine CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
| | - Ian J. Wang
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
| | - Thomas D. Bruns
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
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16
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Livne-Luzon S, Ovadia O, Weber G, Avidan Y, Migael H, Glassman SI, Bruns TD, Shemesh H. Small-scale spatial variability in the distribution of ectomycorrhizal fungi affects plant performance and fungal diversity. Ecol Lett 2017; 20:1192-1202. [DOI: 10.1111/ele.12816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Stav Livne-Luzon
- Department of Life Sciences; Ben-Gurion University of the Negev; POB 653 Beer Sheva Israel
| | - Ofer Ovadia
- Department of Life Sciences; Ben-Gurion University of the Negev; POB 653 Beer Sheva Israel
| | - Gil Weber
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Yael Avidan
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Hen Migael
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Sydney I. Glassman
- Department of Ecology and Evolutionary Biology; UC Irvine; Irvine CA 92697 USA
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology; UC Berkeley; Berkeley CA 94720-3102 USA
| | - Hagai Shemesh
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
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17
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Glassman SI, Lubetkin KC, Chung JA, Bruns TD. The theory of island biogeography applies to ectomycorrhizal fungi in subalpine tree “islands” at a fine scale. Ecosphere 2017. [DOI: 10.1002/ecs2.1677] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sydney I. Glassman
- Department of Ecology and Evolutionary Biology University of California Irvine California 92697 USA
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
| | | | - Judy A. Chung
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
| | - Thomas D. Bruns
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
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18
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Rosenthal LM, Larsson KH, Branco S, Chung JA, Glassman SI, Liao HL, Peay KG, Smith DP, Talbot JM, Taylor JW, Vellinga EC, Vilgalys R, Bruns TD. Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal. Mycologia 2017; 109:115-127. [DOI: 10.1080/00275514.2017.1281677] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lisa M. Rosenthal
- Department of Plant Pathology, University of California Davis, Davis, California 95818
| | | | - Sara Branco
- Ecologie, Systematique et Evolution, Université Paris Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France
| | - Judy A. Chung
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Sydney I. Glassman
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California 94305
| | - Dylan P. Smith
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | | | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Else C. Vellinga
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
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19
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Glassman SI, Levine CR, DiRocco AM, Battles JJ, Bruns TD. Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot. ISME J 2015; 10:1228-39. [PMID: 26473720 DOI: 10.1038/ismej.2015.182] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 08/28/2015] [Accepted: 09/02/2015] [Indexed: 11/09/2022]
Abstract
After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.
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Affiliation(s)
- Sydney I Glassman
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Carrie R Levine
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Angela M DiRocco
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - John J Battles
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Thomas D Bruns
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
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Shrestha P, Ibáñez AB, Bauer S, Glassman SI, Szaro TM, Bruns TD, Taylor JW. Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers. Biotechnol Biofuels 2015; 8:38. [PMID: 25784958 PMCID: PMC4362644 DOI: 10.1186/s13068-015-0221-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/04/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage of the cost of bioethanol production from non-starch (i.e., lignocellulosic) components of energy crops and agricultural residues. We, and others, have reasoned that fungi that naturally deconstruct plant walls may provide the best enzymes for bioconversion of energy crops. RESULTS Previously, we have reported on the isolation of 106 fungi from decaying leaves of Miscanthus and sugarcane (Appl Environ Microbiol 77:5490-504, 2011). Here, we thoroughly analyze 30 of these fungi including those most often found on decaying leaves and stems of these plants, as well as four fungi chosen because they are well-studied for their plant cell wall deconstructing enzymes, for wood decay, or for genetic regulation of plant cell wall deconstruction. We extend our analysis to assess not only their ability over an 8-week period to bioconvert Miscanthus cell walls but also their ability to secrete total protein, to secrete enzymes with the activities of xylanases, exocellulases, endocellulases, and beta-glucosidases, and to remove specific parts of Miscanthus cell walls, that is, glucan, xylan, arabinan, and lignin. CONCLUSION This study of fungi that bioconvert energy crops is significant because 30 fungi were studied, because the fungi were isolated from decaying energy grasses, because enzyme activity and removal of plant cell wall components were recorded in addition to biomass conversion, and because the study period was 2 months. Each of these factors make our study the most thorough to date, and we discovered fungi that are significantly superior on all counts to the most widely used, industrial bioconversion fungus, Trichoderma reesei. Many of the best fungi that we found are in taxonomic groups that have not been exploited for industrial bioconversion and the cultures are available from the Centraalbureau voor Schimmelcultures in Utrecht, Netherlands, for all to use.
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Affiliation(s)
- Prachand Shrestha
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Ana B Ibáñez
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Stefan Bauer
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Sydney I Glassman
- />Department of Environmental Science Policy and Management, University of California, Berkeley, CA 94720 USA
| | - Timothy M Szaro
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Thomas D Bruns
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - John W Taylor
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
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Glassman SI, Peay KG, Talbot JM, Smith DP, Chung JA, Taylor JW, Vilgalys R, Bruns TD. A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern. New Phytol 2015; 205:1619-1631. [PMID: 25557275 DOI: 10.1111/nph.13240] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [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: 07/07/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine-associated ECM fungal spore banks across the North American continent. Soils were collected from 19 plots in forests across North America. Fresh soils were pyrosequenced for fungal internal transcribed spacer (ITS) amplicons. Adjacent soil cores were dried and bioassayed with pine seedlings, and colonized roots were pyrosequenced to detect resistant propagules of ECM fungi. The results showed that ECM spore banks correlated strongly with biogeographic location, but not with the identity of congeneric plant hosts. Minimal community overlap was found between resident ECM fungi vs those in spore banks, and spore bank assemblages were relatively simple and dominated by Rhizopogon, Wilcoxina, Cenococcum, Thelephora, Tuber, Laccaria and Suillus. Similar to plant seed banks, ECM fungal spore banks are, in general, depauperate, and represent a small and rare subset of the mature forest soil fungal community. Yet, they may be extremely important in fungal colonization after large-scale disturbances such as clear cuts and forest fires.
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Affiliation(s)
- Sydney I Glassman
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Jennifer M Talbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Dylan P Smith
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Judy A Chung
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John W Taylor
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Thomas D Bruns
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
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