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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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Karlsen-Ayala E, Jusino MA, Gazis R, Smith ME. Habitat matters: The role of spore bank fungi in early seedling establishment of Florida slash pines. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Miyamoto Y, Maximov TC, Kononov A, Sugimoto A. Soil propagule banks of ectomycorrhizal fungi associated with <i>Larix cajanderi</i> above the treeline in the Siberian Arctic. MYCOSCIENCE 2022; 63:142-148. [PMID: 37090475 PMCID: PMC10042316 DOI: 10.47371/mycosci.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/08/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
Abstract
Microbial symbionts are essential for plant niche expansion into novel habitats. Dormant propagules of ectomycorrhizal (EM) fungi are thought to play an important role in seedling establishment in invasion fronts; however, propagule bank communities above the treeline are poorly understood in the Eurasian Arctic, where treelines are expected to advance under rapid climate change. To investigate the availability of EM fungal propagules, we collected 100 soil samples from Arctic tundra sites and applied bioassay experiments using Larix cajanderi as bait seedlings. We detected 11 EM fungal operational taxonomic units (OTUs) by obtaining entire ITS regions. Suillus clintonianus was the most frequently observed OTU, followed by Cenococcum geophilum and Sebacinales OTU1. Three Suillus and one Rhizopogon species were detected in the bioassay seedlings, indicating the availability of Larix-specific suilloid spores at least 30 km from the contemporary treeline. Spores of S. clintonianus and S. spectabilis remained infective after preservation for 14 mo and heat treatment at 60 °C, implying the durability of the spores. Long-distance dispersal capability and spore resistance to adverse conditions may represent ecological strategies employed by suilloid fungi to quickly associate with emerging seedlings of compatible hosts in treeless habitats.
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Affiliation(s)
| | - Trofim C. Maximov
- Institute for Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences
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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] [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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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] [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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Okada KH, Matsuda Y. Soil spore bank communities of ectomycorrhizal fungi in Pseudotsuga japonica forests and neighboring plantations. MYCORRHIZA 2022; 32:83-93. [PMID: 34989868 DOI: 10.1007/s00572-021-01065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal (EcM) fungal spores play an important role in seedling establishment and forest regeneration, especially in areas where compatible host tree species are absent. However, compared to other Pinaceae trees with a wide distribution, limited information is available for the interaction between the endangered Pseudotsuga trees and EcM fungi, especially the spore bank. The aim of this study was to investigate EcM fungal spore bank communities in soil in remnant patches of Japanese Douglas-fir (Pseudotsuga japonica) forest. We conducted a bioassay of 178 soil samples collected from three P. japonica forests and their neighboring arbuscular mycorrhizal artificial plantations, using the more readily available North American Douglas-fir (Pseudotsuga menziesii) as bait seedlings. EcM fungal species were identified by a combination of morphotyping and DNA sequencing of the ITS region. We found that EcM fungal spore banks were present not only in P. japonica forests but also in neighboring plantations. Among the 13 EcM fungal species detected, Rhizopogon togasawarius had the second highest frequency and was found in all plots, regardless of forest type. Species richness estimators differed significantly among forest types. The community structure of EcM fungal spore banks differed significantly between study sites but not between forest types. These results indicate that EcM fungal spore banks are not restricted to EcM forests and extend to surrounding forest dominated by arbuscular mycorrhizal trees, likely owing to the durability of EcM fungal spores in soils.
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Affiliation(s)
- Keita Henry Okada
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie, 514-8507, Japan.
| | - Yosuke Matsuda
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie, 514-8507, Japan
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Mino L, Kolp MR, Fox S, Reazin C, Zeglin L, Jumpponen A. Watershed and fire severity are stronger determinants of soil chemistry and microbiomes than within-watershed woody encroachment in a tallgrass prairie system. FEMS Microbiol Ecol 2021; 97:6445025. [PMID: 34849770 DOI: 10.1093/femsec/fiab154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fire can impact terrestrial ecosystems by changing abiotic and biotic conditions. Short fire intervals maintain grasslands and communities adapted to frequent, low-severity fires. Shrub encroachment that follows longer fire intervals accumulates fuel and can increase fire severity. This patchily distributed biomass creates mosaics of burn severities in the landscape-pyrodiversity. Afforded by a scheduled burn of a watershed protected from fires for 27 years, we investigated effects of woody encroachment and burn severity on soil chemistry and soil-inhabiting bacteria and fungi. We compared soils before and after fire within the fire-protected, shrub-encroached watershed and soils in an adjacent, annually burned and non-encroached watershed. Organic matter and nutrients accumulated in the fire-protected watershed but responded less to woody encroachment within the encroached watershed. Bioavailable nitrogen and phosphorus and fungal and bacterial communities responded to high-severity burn regardless of encroachment. Low-severity fire effects on soil nutrients differed, increased bacterial but decreased fungal diversity and effects of woody encroachment within the encroached watershed were minimal. High-severity burns in the fire-protected watershed led to a novel soil system state distinct from non-encroached and encroached soil systems. We conclude that severe fires may open grassland restoration opportunities to manipulate soil chemistry and microbial communities in shrub-encroached habitats.
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Affiliation(s)
- Laura Mino
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Matthew R Kolp
- Department of Microbiology, University of Tennessee, 520B Ken and Blaire Mossman Bldg, 1311 Cumberland Ave, Knoxville, TN 37996, USA
| | - Sam Fox
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Chris Reazin
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Lydia Zeglin
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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Miyamoto Y, Danilov AV, Bryanin SV. The dominance of Suillus species in ectomycorrhizal fungal communities on Larix gmelinii in a post-fire forest in the Russian Far East. MYCORRHIZA 2021; 31:55-66. [PMID: 33159597 DOI: 10.1007/s00572-020-00995-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/17/2020] [Indexed: 06/11/2023]
Abstract
Wildfires can negatively affect ectomycorrhizal (EM) fungal communities. However, potential shifts in community structures due to wildfires have rarely been evaluated in the forests of eastern Eurasia, where surface fires are frequent. We investigated EM fungal communities in a Larix gmelinii-dominated forest that burned in 2003 in Zeya, in the Russian Far East. A total of 120 soil samples were collected from burned and adjacent unburned forest sites. The EM fungal root tips were morphotyped and internal transcribed spacer (ITS) sequences were obtained for fungal identification. We detected 147 EM fungal operational taxonomic units, and EM fungal richness was 25% lower at the burned site than at the unburned site. EM fungal composition was characterized by the occurrence of disturbance-adapted fungi (Amphinema and Wilcoxina) at the burned site and late-successional fungi (Lactarius, Russula and Cortinarius) at the unburned site. These findings suggest that the EM fungal communities did not recover to pre-fire levels 16 years after the fire. Suillus species were the dominant EM fungi on L. gmelinii, with greater richness and frequency at the burned site. Both Larix and Suillus exhibit adaptive traits to quickly colonize fire-disturbed habitats. Frequent surface fires common to eastern Eurasia are likely to play important roles in maintaining Larix forests, concomitantly with their closely associated EM fungi.
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Affiliation(s)
- Yumiko Miyamoto
- Arctic Research Center, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Aleksandr V Danilov
- Institute of Geology and Nature Management, Far East Branch, Russian Academy of Sciences, Blagoveshchensk, Russia
| | - Semyon V Bryanin
- Institute of Geology and Nature Management, Far East Branch, Russian Academy of Sciences, Blagoveshchensk, Russia
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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] [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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