1
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Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. New Phytol 2024; 242:1825-1834. [PMID: 37929750 DOI: 10.1111/nph.19385] [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: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
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Affiliation(s)
- Deyi Wang
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, 2333 CC, Leiden University, Leiden, the Netherlands
| | - Sofia I F Gomes
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, 3001, Leuven, Belgium
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
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2
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Kokkoris V, Banchini C, Paré L, Abdellatif L, Séguin S, Hubbard K, Findlay W, Dalpé Y, Dettman J, Corradi N, Stefani F. Rhizophagus irregularis, the model fungus in arbuscular mycorrhiza research, forms dimorphic spores. New Phytol 2024; 242:1771-1784. [PMID: 37434339 DOI: 10.1111/nph.19121] [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: 05/04/2023] [Accepted: 06/10/2023] [Indexed: 07/13/2023]
Abstract
Rhizophagus irregularis is the model species for arbuscular mycorrhizal fungi (AMF) research and the most widely propagated species for commercial plant biostimulants. Using asymbiotic and symbiotic cultivation systems initiated from single spores, advanced microscopy, Sanger sequencing of the glomalin gene, and PacBio sequencing of the partial 45S rRNA gene, we show that four strains of R. irregularis produce spores of two distinct morphotypes, one corresponding to the morphotype described in the R. irregularis protologue and the other having the phenotype of R. fasciculatus. The two spore morphs are easily distinguished by spore colour, thickness of the subtending hypha, thickness of the second wall layer, lamination of the innermost layer, and the dextrinoid reaction of the two outer spore wall layers to Melzer's reagent. The glomalin gene of the two spore morphs is identical and that of the PacBio sequences of the partial SSU-ITS-LSU region (2780 bp) obtained from single spores of the R. cf fasciculatus morphotype has a median pairwise similarity of 99.8% (SD = 0.005%) to the rDNA ribotypes of R. irregularis DAOM 197198. Based on these results, we conclude that the model AMF species R. irregularis is dimorphic, which has caused taxonomic confusion in culture collections and possibly in AMF research.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Claudia Banchini
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Louis Paré
- Université Laval, Centre d'Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Lobna Abdellatif
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Keith Hubbard
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Wendy Findlay
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
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3
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Lofgren L, Nguyen NH, Kennedy PG, 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. New Phytol 2024; 242:1448-1475. [PMID: 38581203 DOI: 10.1111/nph.19700] [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: 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 G 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
| | - 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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4
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytol 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [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: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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5
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Auer L, Buée M, Fauchery L, Lombard V, Barry KW, Clum A, Copeland A, Daum C, Foster B, LaButti K, Singan V, Yoshinaga Y, Martineau C, Alfaro M, Castillo FJ, Imbert JB, Ramírez L, Castanera R, Pisabarro AG, Finlay R, Lindahl B, Olson A, Séguin A, Kohler A, Henrissat B, Grigoriev IV, Martin FM. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New Phytol 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [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: 05/22/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023]
Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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Affiliation(s)
- Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, 13288, France
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, 13009, France
| | - Kerry W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Federico J Castillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - J Bosco Imbert
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Lucia Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Roger Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Björn Lindahl
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Bernard Henrissat
- DTU Bioengineering, Denmarks Tekniske Universitet, Copenhagen, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
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Ledford WC, Silvestri A, Fiorilli V, Roth R, Rubio-Somoza I, Lanfranco L. A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis. New Phytol 2024; 242:1534-1544. [PMID: 37985403 DOI: 10.1111/nph.19394] [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: 07/31/2023] [Accepted: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.
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Affiliation(s)
- William Conrad Ledford
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Alessandro Silvestri
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08001, Spain
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
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Wang L, George TS, Feng G. Concepts and consequences of the hyphosphere core microbiome for arbuscular mycorrhizal fungal fitness and function. New Phytol 2024; 242:1529-1533. [PMID: 38044555 DOI: 10.1111/nph.19396] [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: 07/21/2023] [Accepted: 10/15/2023] [Indexed: 12/05/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiomes can be considered as the second genome of the mycorrhizal phosphorus uptake pathway. Their composition can be thought of as a stably recurring component of a holobiont, defined by the hyphosphere core microbiome, which is thought to benefit AM fungal fitness. Here, we review evidence indicating the existence of the hyphosphere core microbiome, highlight its functions linked to those functions lacking in AM fungi, and further explore the mechanisms by which different core members ensure their stable coexistence. We conclude that deciphering and utilizing the hyphosphere core microbiome provides an entry point for understanding the complex interactions among plants, AM fungi, and bacteria.
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Affiliation(s)
- Letian Wang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | | | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
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8
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Mudbhari S, Lofgren L, Appidi MR, Vilgalys R, Hettich RL, Abraham PE. Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity. mSystems 2024; 9:e0122523. [PMID: 38470040 PMCID: PMC11019867 DOI: 10.1128/msystems.01225-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon. Suillus are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three Suillus species (Suillus hirtellus EM16, Suillus decipiens EM49, and Suillus cothurnatus VC1858), core members of the pine microbiome. After 28 days of growth on solid media, liquid chromatography-tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between Suillus co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 41 putative prenol lipids (includes 37 putative terpenes) were identified across the three Suillus species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and Suillus spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication.IMPORTANCEUsing a combination of genomics and metabolomics, this study's findings offer new insights into the chemical diversity of Suillus fungi, which serve a critical role in forest ecosystems.
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Affiliation(s)
- Sameer Mudbhari
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lotus Lofgren
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Manasa R. Appidi
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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9
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Djotan AKG, Matsushita N, Fukuda K. Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica. Mycorrhiza 2024; 34:119-130. [PMID: 38509266 PMCID: PMC10998819 DOI: 10.1007/s00572-024-01143-x] [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: 12/23/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.
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Affiliation(s)
- Akotchiffor Kevin Geoffroy Djotan
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
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Sanchez-Tello JD, Corrales A. Ectomycorrhizal fungal communities in natural and urban ecosystems: Quercus humboldtii as a study case in the tropical Andes. Mycorrhiza 2024; 34:45-55. [PMID: 38483629 PMCID: PMC10998789 DOI: 10.1007/s00572-024-01140-0] [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: 07/20/2023] [Accepted: 02/22/2024] [Indexed: 04/07/2024]
Abstract
Worldwide urban landscapes are expanding because of the growing human population. Urban ecosystems serve as habitats to highly diverse communities. However, studies focusing on the diversity and structure of ectomycorrhizal communities are uncommon in this habitat. In Colombia, Quercus humboldtii Bonpl. is an ectomycorrhizal tree thriving in tropical montane forests hosting a high diversity of ectomycorrhizal fungi. Q. humboldtii is planted as an urban tree in Bogotá (Colombia). We studied how root-associated fungal communities of this tree change between natural and urban areas. Using Illumina sequencing, we amplified the ITS1 region and analyzed the resulting data using both OTUs and Amplicon Sequence Variants (ASVs) bioinformatics pipelines. The results obtained using both pipelines showed no substantial differences between OTUs and ASVs for the community patterns of root-associated fungi, and only differences in species richness were observed. We found no significant differences in the species richness between urban and rural sites based on Fisher's alpha or species-accumulation curves. However, we found significant differences in the community composition of fungi present in the roots of rural and urban trees with rural communities being dominated by Russula and Lactarius and urban communities by Scleroderma, Hydnangium, and Trechispora, suggesting a high impact of urban disturbances on ectomycorrhizal fungal communities. Our results highlight the importance of urban trees as reservoirs of fungal diversity and the potential impact of urban conditions on favoring fungal species adapted to more disturbed ecosystems.
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Affiliation(s)
- Juan David Sanchez-Tello
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia.
| | - Adriana Corrales
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Society for the Protection of Underground Networks, SPUN, 3500 South DuPont Highway, Dover, DE, 19901, USA
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11
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Mujica MI, Herrera H, Cisternas M, Zuniga-Feest A, Sagredo-Saez C, Selosse MA. Mycorrhizas in South American Ericaceae. Mycorrhiza 2024; 34:1-18. [PMID: 38512497 DOI: 10.1007/s00572-024-01141-z] [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: 12/08/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Mycorrhizal symbioses (mycorrhizas) of Ericaceae, including ericoid mycorrhiza (ErM), have been mainly studied in the Northern Hemisphere, although the highest diversity of ericaceous plants is located in the Southern Hemisphere, where several regions remain largely unexplored. One of them is South America, which harbors a remarkably high diversity of Ericaceae (691 species and 33 genera) in a wide range of environmental conditions, and a specific mycorrhizal type called cavendishioid. In this review, we compile all available information on mycorrhizas of Ericaceae in South America. We report data on the mycorrhizal type and fungal diversity in 17 and 11 ericaceous genera, respectively. We show that South American Ericaceae exhibit a high diversity of habitats and life forms and that some species from typical ErM subfamilies may also host arbuscular mycorrhiza. Also, a possible geographical pattern in South American ErM fungal communities is suggested, with Sebacinales being the dominant mycorrhizal partners of the Andean clade species from tropical mountains, while archetypal ErM fungi are common partners in southern South America species. The gathered information challenges some common assumptions about ErM and suggests that focusing on understudied regions would improve our understanding of the evolution of mycorrhizal associations in this intriguing family.
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Affiliation(s)
- María Isabel Mujica
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
| | - Héctor Herrera
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Mauricio Cisternas
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, La Cruz, Chile
| | - Alejandra Zuniga-Feest
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristiane Sagredo-Saez
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (UMR 7205-CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005, Paris, France
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
- Institut Universitaire de France (IUF), Paris, France
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12
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Marqués-Gálvez JE, Pandharikar G, Basso V, Kohler A, Lackus ND, Barry K, Keymanesh K, Johnson J, Singan V, Grigoriev IV, Vilgalys R, Martin F, Veneault-Fourrey C. Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. New Phytol 2024; 242:658-674. [PMID: 38375883 DOI: 10.1111/nph.19609] [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: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024]
Abstract
The jasmonic acid (JA) signalling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis. The Laccaria bicolor effector MiSSP7 stabilizes JA corepressor JAZ6, thereby inhibiting the activity of Populus MYC2 transcription factors. Although the role of MYC2 in orchestrating plant defences against pathogens is well established, its exact contribution to ECM symbiosis remains unclear. This information is crucial for understanding the balance between plant immunity and symbiotic relationships. Transgenic poplars overexpressing or silencing for the two paralogues of MYC2 transcription factor (MYC2s) were produced, and their ability to establish ectomycorrhiza was assessed. Transcriptomics and DNA affinity purification sequencing were performed. MYC2s overexpression led to a decrease in fungal colonization, whereas its silencing increased it. The enrichment of terpene synthase genes in the MYC2-regulated gene set suggests a complex interplay between the host monoterpenes and fungal growth. Several root monoterpenes have been identified as inhibitors of fungal growth and ECM symbiosis. Our results highlight the significance of poplar MYC2s and terpenes in mutualistic symbiosis by controlling root fungal colonization. We identified poplar genes which direct or indirect control by MYC2 is required for ECM establishment. These findings deepen our understanding of the molecular mechanisms underlying ECM symbiosis.
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Affiliation(s)
- José Eduardo Marqués-Gálvez
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Gaurav Pandharikar
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Veronica Basso
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Nathalie D Lackus
- Lehrstuhl für Pharmazeutische Biologie, Julius-von-Sachs-Institut für Biowissenschaften, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs-Platz 2, Würzburg, 97082, Deutschland
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
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13
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Tedersoo L, Drenkhan R, Abarenkov K, Anslan S, Bahram M, Bitenieks K, Buegger F, Gohar D, Hagh‐Doust N, Klavina D, Makovskis K, Zusevica A, Pritsch K, Padari A, Põlme S, Rahimlou S, Rungis D, Mikryukov V. The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi. Environ Microbiol Rep 2024; 16:e13253. [PMID: 38575147 PMCID: PMC10994715 DOI: 10.1111/1758-2229.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mohammad Bahram
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Kriss Bitenieks
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Franz Buegger
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Niloufar Hagh‐Doust
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Kristaps Makovskis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Austra Zusevica
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Karin Pritsch
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Allar Padari
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Natural History MuseumUniversity of TartuTartuEstonia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Dainis Rungis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Vladimir Mikryukov
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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14
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Šibanc N, Clark DR, Helgason T, Dumbrell AJ, Maček I. Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi. mSystems 2024; 9:e0133123. [PMID: 38376262 PMCID: PMC10949450 DOI: 10.1128/msystems.01331-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem-mofettes or natural CO2 springs caused by geological CO2 exhalations-are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, "stress tolerant" taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.IMPORTANCEArbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.
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Affiliation(s)
- Nataša Šibanc
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of forest physiology and genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Colchester, United Kingdom
| | - Thorunn Helgason
- Department of Biology, University of York, York, United Kingdom
- Institute for Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Alex J. Dumbrell
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Irena Maček
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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15
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Matteoli FP, Silva AMM, de Araújo VLVP, Feiler HP, Cardoso EJBN. Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks. World J Microbiol Biotechnol 2024; 40:119. [PMID: 38429532 DOI: 10.1007/s11274-024-03926-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.
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Affiliation(s)
- Filipe Pereira Matteoli
- Laboratory of Microbial Bioinformatics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru, Brazil.
| | - Antonio M M Silva
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Victor L V P de Araújo
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Henrique P Feiler
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Elke J B N Cardoso
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
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16
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Martinez A, Schiro G, Barberán A. Soil microbial communities along elevational gradients in the Madrean Sky Islands. Environ Microbiol 2024; 26:e16596. [PMID: 38387888 DOI: 10.1111/1462-2920.16596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
The Madrean Sky Islands are mountain ranges isolated by a 'desert sea'. This area is a biodiversity hotspot currently threatened by climate change. Here, we studied soil microbial communities along elevational gradients in eight Madrean Sky Islands in southeastern Arizona (USA). Our results showed that while elevational microbial richness gradients were weak and not consistent across different mountains, soil properties strongly influenced microbial community composition (overall composition and the abundance of key functional groups) along elevational gradients. In particular, warming is associated with a higher abundance of soil-borne fungal plant pathogens that concomitantly might facilitate upward elevational shifts of plant species released from negative plant-soil feedbacks. Furthermore, projected warming and drought in the area aggravated by anthropogenic nitrogen deposition on mountain tops (and thus, decreasing nitrogen limitation) can enhance a shift from ectomycorrhizal to arbuscular mycorrhizal fungi. Overall, these results indicate that climate change effects on plant-soil interactions might have profound ecosystem consequences.
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Affiliation(s)
- Adalee Martinez
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
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17
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de Pontes JS, Oehl F, Pereira CD, de Toledo Machado CT, Coyne D, da Silva DKA, Maia LC. Heterogeneity in Arbuscular Mycorrhizal Fungi and Plant Communities of the Brazilian Cerrado, Transitional Areas toward the Caatinga, and the Atlantic Forest. Microb Ecol 2024; 87:29. [PMID: 38191681 DOI: 10.1007/s00248-023-02337-0] [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: 09/13/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
The Cerrado is the most diverse tropical savanna worldwide and the second-largest biome in South America. The objective of this study was to understand the heterogeneity and dynamics of arbuscular mycorrhizal fungi (AMF) in different types of natural Cerrado vegetation and areas that are transitioning to dryer savannas or tropical rainforests and to elucidate the driving factors responsible for the differences between these ecosystems. Twenty-one natural sites were investigated, including typical Cerrado forest, typical Caatinga, Atlantic Rainforest, transitions between Cerrado and Caatinga, Cerrado areas near Caatinga or rainforest, and Carrasco sites. Spores were extracted from the soils, counted, and morphologically analyzed. In total, 82 AMF species were detected. AMF species richness varied between 36 and 51, with the highest richness found in the area transitioning between Cerrado and Caatinga, followed by areas of Cerrado close to Caatinga and typical Cerrado forest. The types of Cerrado vegetation and the areas transitioning to the Caatinga shared the highest numbers of AMF species (32-38). Vegetation, along with chemical and physical soil parameters, affected the AMF communities, which may also result from seasonal rainfall patterns. The Cerrado has a great AMF diversity and is, consequently, a natural refuge for AMF. The plant and microbial communities as well as the diversity of habitats require urgent protection within the Cerrado, as it represents a key AMF hotspot.
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Affiliation(s)
- Juliana Souza de Pontes
- Programa de Pós-Graduação em Ciências Biológicas, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, PE, 50740-600, Brazil
| | - Fritz Oehl
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, PE, 50740-600, Brazil
- Agroscope, Competence Division of Plants and Plant Products, Plant Protection Products-Impact and Assessment, Müller-Thurgau-Strasse 29, CH-8820, Wädenswil, Switzerland
| | | | | | - Danny Coyne
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
| | - Danielle Karla Alves da Silva
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, PE, 50740-600, Brazil.
| | - Leonor Costa Maia
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Recife, PE, 50740-600, Brazil
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18
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Větrovský T, Kolaříková Z, Lepinay C, Awokunle Hollá S, Davison J, Fleyberková A, Gromyko A, Jelínková B, Kolařík M, Krüger M, Lejsková R, Michalčíková L, Michalová T, Moora M, Moravcová A, Moulíková Š, Odriozola I, Öpik M, Pappová M, Piché-Choquette S, Skřivánek J, Vlk L, Zobel M, Baldrian P, Kohout P. GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies. New Phytol 2023; 240:2151-2163. [PMID: 37781910 DOI: 10.1111/nph.19283] [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: 04/11/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Anna Fleyberková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Anastasiia Gromyko
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Barbora Jelínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Manuela Krüger
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Renata Lejsková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Andrea Moravcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Štěpánka Moulíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Monika Pappová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Jakub Skřivánek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
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19
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Keller-Pearson M, Bortolazzo A, Willems L, Smith B, Peterson A, Ané JM, Silva EM. A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot. Mol Plant Microbe Interact 2023; 36:821-832. [PMID: 37698455 DOI: 10.1094/mpmi-04-23-0038-r] [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] [Indexed: 09/13/2023]
Abstract
While arbuscular mycorrhizal (AM) fungi are known for providing host plants with improved drought tolerance, we know very little about the fungal response to drought in the context of the fungal-plant relationship. In this study, we evaluated the drought responses of the host and symbiont, using the fungus Rhizophagus irregularis with carrot (Daucus carota) as a plant model. Carrots inoculated with spores of R. irregularis DAOM 197198 were grown in a greenhouse. During taproot development, carrots were exposed to a 10-day water restriction. Compared with well-watered conditions, drought caused diminished photosynthetic activity and reduced plant growth in carrot with and without AM fungi. Droughted carrots had lower root colonization. For R. irregularis, 93% of 826 differentially expressed genes (DEGs) were upregulated during drought, including phosphate transporters, several predicted transport proteins of potassium, and the aquaporin RiAQPF2. In contrast, 78% of 2,486 DEGs in AM carrot were downregulated during drought, including the symbiosis-specific genes FatM, RAM2, and STR, which are implicated in lipid transfer from the host to the fungus and were upregulated exclusively in AM carrot during well-watered conditions. Overall, this study provides insight into the drought response of an AM fungus in relation to its host; the expression of genes related to symbiosis and nutrient exchange were downregulated in carrot but upregulated in the fungus. This study reveals that carrot and R. irregularis exhibit contrast in their regulation of gene expression during drought, with carrot reducing its apparent investment in symbiosis and the fungus increasing its apparent symbiotic efforts. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Anthony Bortolazzo
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Luke Willems
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Brendan Smith
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Annika Peterson
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Erin M Silva
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, U.S.A
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20
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Tao Y, Li C, Liu Y, Xu C, Okabe S, Matsushita N, Lian C. Identification of microRNAs involved in ectomycorrhizal formation in Populus tomentosa. Tree Physiol 2023; 43:2012-2030. [PMID: 37777191 DOI: 10.1093/treephys/tpad102] [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: 01/29/2023] [Accepted: 08/17/2023] [Indexed: 10/02/2023]
Abstract
The majority of woody plants are able to form ectomycorrhizal (ECM) symbioses with fungi. During symbiotic development, plants undergo a complex re-programming process involving a series of physiological and morphological changes. MicroRNAs (miRNAs) are important components of the regulatory network underlying symbiotic development. To elucidate the mechanisms of miRNAs and miRNA-mediated mRNA cleavage during symbiotic development, we conducted high-throughput sequencing of small RNAs and degradome tags from roots of Populus tomentosa inoculated with Cenococcum geophilum. This process led to the annotation of 51 differentially expressed miRNAs between non-mycorrhizal and mycorrhizal roots of P. tomentosa, including 13 novel miRNAs. Increased or decreased accumulation of several novel and conserved miRNAs in ECM roots, including miR162, miR164, miR319, miR396, miR397, miR398, novel-miR44 and novel-miR47, suggests essential roles for these miRNAs in ECM formation. The degradome analysis identified root transcripts as miRNA-mediated mRNA cleavage targets, which was confirmed using real-time quantitative PCR. Several of the identified miRNAs and corresponding targets are involved in arbuscular mycorrhizal symbioses. In summary, increased or decreased accumulation of specific miRNAs and miRNA-mediated cleavage of symbiosis-related genes indicate that miRNAs play important roles in the regulatory network underlying symbiotic development.
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Affiliation(s)
- Yuanxun Tao
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Chaofeng Li
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
- Maize Research Institute, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Ying Liu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Shin Okabe
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
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21
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Xia G, Zhu S, Zhao W, Yang X, Sheng L, Mao H. Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance. PeerJ 2023; 11:e15681. [PMID: 37953782 PMCID: PMC10638908 DOI: 10.7717/peerj.15681] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/13/2023] [Indexed: 11/14/2023] Open
Abstract
To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress.
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Affiliation(s)
- Guodong Xia
- Guizhou Minzu University, The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang, Guizhou, China
| | - Sixi Zhu
- Guizhou Minzu University, The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang, Guizhou, China
| | - Wei Zhao
- Guizhou Minzu University, The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang, Guizhou, China
| | - Xiuqing Yang
- Guizhou Minzu University, Guiyang, Guizhou, China
| | - Luying Sheng
- Guizhou Minzu University, The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang, Guizhou, China
| | - Huan Mao
- Guizhou Minzu University, The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang, Guizhou, China
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22
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Shirakawa M, Matsushita N, Fukuda K. Visualization of root extracellular traps in an ectomycorrhizal woody plant (Pinus densiflora) and their interactions with root-associated bacteria. Planta 2023; 258:112. [PMID: 37935872 PMCID: PMC10630192 DOI: 10.1007/s00425-023-04274-1] [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: 07/14/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
MAIN CONCLUSION Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants.
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Affiliation(s)
- Makoto Shirakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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23
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Afshana, Reshi ZA, Shah MA, Malik RA, Rashid I. Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya. Int Microbiol 2023; 26:1053-1071. [PMID: 37093323 DOI: 10.1007/s10123-023-00359-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/08/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.
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Affiliation(s)
- Afshana
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India.
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Rayees A Malik
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
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24
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Sperschneider J, Yildirir G, Rizzi YS, Malar C M, Mayrand Nicol A, Sorwar E, Villeneuve-Laroche M, Chen ECH, Iwasaki W, Brauer EK, Bosnich W, Gutjahr C, Corradi N. Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host-plant interactions. Nat Microbiol 2023; 8:2142-2153. [PMID: 37884816 DOI: 10.1038/s41564-023-01495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts that can carry thousands of nuclei deriving from two parental strains in a large syncytium. These co-existing genomes can also vary in abundance with changing environmental conditions. Here we assemble the nuclear genomes of all four publicly available AMF heterokaryons using PacBio high-fidelity and Hi-C sequencing. We find that the two co-existing genomes of these strains are phylogenetically related but differ in structure, content and epigenetics. We confirm that AMF heterokaryon genomes vary in relative abundance across conditions and show this can lead to nucleus-specific differences in expression during interactions with plants. Population analyses also reveal signatures of genetic exchange indicative of past events of sexual reproduction in these strains. This work uncovers the origin and contribution of two nuclear genomes in AMF heterokaryons and opens avenues for the improvement and environmental application of these strains.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Yanina S Rizzi
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Eric C H Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Elizabeth K Brauer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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25
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Terry V, Kokkoris V, Villeneuve-Laroche M, Turcu B, Chapman K, Cornell C, Zheng Z, Stefani F, Corradi N. Mycorrhizal response of Solanum tuberosum to homokaryotic versus dikaryotic arbuscular mycorrhizal fungi. Mycorrhiza 2023; 33:333-344. [PMID: 37572110 DOI: 10.1007/s00572-023-01123-7] [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: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts of most land plants. In these organisms, thousands of nuclei that are either genetically similar (homokaryotic) or derived from two distinct parents (dikaryotic) co-exist in a large syncytium. Here, we investigated the impact of these two nuclear organizations on the mycorrhizal response of potatoes (Solanum tuberosum) by inoculating four potato cultivars with eight Rhizophagus irregularis strains individually (four homokaryotic and four dikaryotic). By evaluating plant and fungal fitness-related traits four months post inoculation, we found that AMF genetic organization significantly affects the mycorrhizal response of host plants. Specifically, homokaryotic strains lead to higher total, shoot, and tuber biomass and a higher number of tubers, compared to dikaryotic strains. However, fungal fitness-related traits showed no clear differences between homokaryotic and dikaryotic strains. Nucleotype content analysis of single spores confirmed that the nucleotype ratio of AMF heterokaryon spores can shift depending on host identity. Together, these findings continue to highlight significant ecological differences derived from the two distinct genetic organizations in AMF.
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Affiliation(s)
- Victoria Terry
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Present address: Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Present address: Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | | | - Bianca Turcu
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Kendyll Chapman
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Calvin Cornell
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Zhiming Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Franck Stefani
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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26
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Vohník M, Bruzone MC, Knoblochová T, Fernández NV, Kolaříková Z, Větrovský T, Fontenla SB. Exploring structural and molecular diversity of Ericaceae hair root mycobionts: a comparison between Northern Bohemia and Argentine Patagonia. Mycorrhiza 2023; 33:425-447. [PMID: 37792114 DOI: 10.1007/s00572-023-01125-5] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023]
Abstract
Core Ericaceae produce delicate hair roots with inflated rhizodermal cells that host plethora of fungal symbionts. These poorly known mycobionts include various endophytes, parasites, saprobes, and the ericoid mycorrhizal (ErM) fungi (ErMF) that form the ErM symbiosis crucial for the fitness of their hosts. Using microscopy and high-throughput sequencing, we investigated their structural and molecular diversity in 14 different host × site combinations in Northern Bohemia (Central Europe) and Argentine Patagonia (South America). While we found typical ericoid mycorrhiza in all combinations, we did not detect ectomycorrhiza and arbuscular mycorrhiza. Superficial mantles of various thickness formed by non-clamped hyphae were observed in all combinations except Calluna vulgaris from N. Bohemia. Some samples contained frequent intercellular hyphae while others possessed previously unreported intracellular haustoria-like structures linked with intracellular hyphal coils. The 711 detected fungal OTU were dominated by Ascomycota (563) and Basidiomycota (119), followed by four other phyla. Ascomycetes comprised Helotiales (255), Pleosporales (53), Chaetothyriales (42), and other 19 orders, while basidiomycetes Sebacinales (42), Agaricales (28), Auriculariales (7), and other 14 orders. While many dominant OTU from both hemispheres lacked close relatives in reference databases, many were very similar to identical to unnamed sequences from around the world. On the other hand, several significant ericaceous mycobionts were absent in our dataset, incl. Cairneyella, Gamarada, Kurtia, Lachnum, and Leohumicola. Most of the detected OTU could not be reliably linked to a particular trophic mode, and only two could be reliably assigned to the archetypal ErMF Hyaloscypha hepaticicola. Probable ErMF comprised Hyaloscypha variabilis and Oidiodendron maius, both detected only in N. Bohemia. Possible ErMF comprised sebacinoid fungi and several unnamed members of Hyaloscypha s. str. While H. hepaticicola was dominant only in C. vulgaris, this model ErM host lacked O. maius and sebacinoid mycobionts. Hyaloscypha hepaticicola was absent in two and very rare in six combinations from Patagonia. Nine OTU represented dark septate endophytes from the Phialocephala fortinii s. lat.-Acephala applanata species complex, including the most abundant OTU (the only detected in all combinations). Statistical analyses revealed marked differences between N. Bohemia and Patagonia, but also within Patagonia, due to the unique community detected in a Valdivian temperate rainforest. Our results show that the ericaceous hair roots may host diverse mycobionts with mostly unknown functions and indicate that many novel ErMF lineages await discovery. Transhemispheric differences (thousands of km) in their communities may be evenly matched by local differences (scales of km, m, and less).
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Affiliation(s)
- Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia.
| | - M Clara Bruzone
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
| | - Tereza Knoblochová
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Natalia V Fernández
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Zuzana Kolaříková
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Sonia B Fontenla
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
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27
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Schulz G, Camenzind T, Sánchez-Galindo LM, Schneider D, Scheu S, Krashevska V. Response of protists to nitrogen addition, arbuscular mycorrhizal fungi manipulation, and mesofauna reduction in a tropical montane rainforest in southern Ecuador. J Eukaryot Microbiol 2023; 70:e12996. [PMID: 37577763 DOI: 10.1111/jeu.12996] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
The tropical Andes are a species-rich and nitrogen-limited system, susceptible to increased nitrogen (N) inputs from the atmosphere. However, our understanding of the impacts of increased N input on belowground systems, in particular on protists and their role in nutrient cycling, remains limited. We explored how increased N affects protists in tropical montane rainforests in Ecuador using high-throughput sequencing (HTS) of environmental DNA from two litter layers. In addition, we manipulated the amount of arbuscular mycorrhizal fungi (AMF) and mesofauna, both playing a significant role in N cycling and interacting in complex ways with protist communities. We found that N strongly affected protist community composition in both layers, while mesofauna reduction had a stronger effect on the lower layer. Changes in concentration of the AMF marker lipid had little effect on protists. In both layers, the addition of N increased phagotrophs and animal parasites and decreased plant parasites, while mixotrophs decreased in the upper layer but increased in the lower layer. In the upper layer with higher AMF concentration, mixotrophs decreased, while in the lower layer, photoautotrophs increased and plant parasites decreased. With reduced mesofauna, phagotrophs increased and animal parasites decreased in both layers, while plant parasites increased only in the upper layer. The findings indicate that to understand the intricate response of protist communities to environmental changes, it is critical to thoroughly analyze these communities across litter and soil layers, and to include HTS.
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Affiliation(s)
- Garvin Schulz
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Laura M Sánchez-Galindo
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Goettingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Valentyna Krashevska
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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28
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Corona Ramírez A, Symanczik S, Gallusser T, Bodenhausen N. Quantification of arbuscular mycorrhizal fungi root colonization in wheat, tomato, and leek using absolute qPCR. Mycorrhiza 2023; 33:387-397. [PMID: 37646822 PMCID: PMC10752845 DOI: 10.1007/s00572-023-01122-8] [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: 04/12/2023] [Accepted: 07/13/2023] [Indexed: 09/01/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and are known to have a positive effect on plant growth and health. Different methodologies have been developed to assess the AMF-plant symbiosis. The most applied method, which involves staining of roots and microscopic observation of the AMF structures, is tedious and time-consuming and the results are highly dependent on the observer. Using quantitative polymerase chain reaction (qPCR) to quantify AMF root colonization represents a reliable, high-throughput technique that allows the assessment of numerous samples. Quantification with qPCR can be performed through two methods: relative quantification and absolute quantification. In relative quantification, the target gene is normalized with a reference gene. On the other hand, absolute quantification involves the use of a standard curve, for which template DNA is serially diluted. In a previous paper, we validated the primer pair AMG1F and AM1 for a relative quantification approach to assess AMF root colonization in Petunia. Here, we tested the same primers with an absolute quantification approach and compared the results with the traditional microscopy method. We evaluated the qPCR method with three different crops, namely, wheat (cv. Colmetta and Wiwa), tomato, and leek. We observed a strong correlation between microscopy and qPCR for Colmetta (r = 0.90, p < 0.001), Wiwa (r = 0.94, p < 0.001), and tomato (r = 0.93, p < 0.001), but no correlation for leek (r = 0.27, p = 0.268). This highlights the importance of testing the primer pair for each specific crop.
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Affiliation(s)
- Andrea Corona Ramírez
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Sarah Symanczik
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Tabea Gallusser
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland.
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29
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Meng Y, Davison J, Clarke JT, Zobel M, Gerz M, Moora M, Öpik M, Bueno CG. Environmental modulation of plant mycorrhizal traits in the global flora. Ecol Lett 2023; 26:1862-1876. [PMID: 37766496 DOI: 10.1111/ele.14309] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Mycorrhizal symbioses are known to strongly influence plant performance, structure plant communities and shape ecosystem dynamics. Plant mycorrhizal traits, such as those characterising mycorrhizal type (arbuscular (AM), ecto-, ericoid or orchid mycorrhiza) and status (obligately (OM), facultatively (FM) or non-mycorrhizal) offer valuable insight into plant belowground functionality. Here, we compile available plant mycorrhizal trait information and global occurrence data (∼ 100 million records) for 11,770 vascular plant species. Using a plant phylogenetic mega-tree and high-resolution climatic and edaphic data layers, we assess phylogenetic and environmental correlates of plant mycorrhizal traits. We find that plant mycorrhizal type is more phylogenetically conserved than plant mycorrhizal status, while environmental variables (both climatic and edaphic; notably soil texture) explain more variation in mycorrhizal status, especially FM. The previously underestimated role of environmental conditions has far-reaching implications for our understanding of ecosystem functioning under changing climatic and soil conditions.
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Affiliation(s)
- Yiming Meng
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - John T Clarke
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Pyrenean Institute of Ecology, IPE-CSIC, Jaca, Spain
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30
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Li M, Perez-Limón S, Ramírez-Flores MR, Barrales-Gamez B, Meraz-Mercado MA, Ziegler G, Baxter I, Olalde-Portugal V, Sawers RJH. Mycorrhizal status and host genotype interact to shape plant nutrition in field grown maize (Zea mays ssp. mays). Mycorrhiza 2023; 33:345-358. [PMID: 37851276 PMCID: PMC10752836 DOI: 10.1007/s00572-023-01127-3] [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: 05/20/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbioses with the major cereal crops, providing plants with increased access to nutrients while enhancing their tolerance to toxic heavy metals. However, not all plant varieties benefit equally from this association. In this study, we used quantitative trait loci (QTL) mapping to evaluate the combined effect of host genotypic variation (G) and AMF across 141 genotypes on the concentration of 20 mineral elements in the leaves and grain of field grown maize (Zea mays spp. mays). Our mapping design included selective incorporation of a castor AMF-incompatibility mutation, allowing estimation of AMF, QTL and QTLxAMF effects by comparison of mycorrhizal and non-mycorrhizal plants. Overall, AMF compatibility was associated with higher concentrations of boron (B), copper (Cu), molybdenum (Mo), phosphorus (P), selenium (Se) and zinc (Zn) and lower concentrations of arsenic (As), iron (Fe), magnesium (Mg), manganese (Mn), potassium (K) and strontium (Sr). In addition to effects on individual elements, pairwise correlation matrices for element concentration differed between mycorrhizal and non-mycorrhizal plants. We mapped 22 element QTLs, including 18 associated with QTLxAMF effects that indicate plant genotype-specific differences in the impact of AMF on the host ionome. Although there is considerable interest in AMF as biofertilizers, it remains challenging to estimate the impact of AMF in the field. Our design illustrates an effective approach for field evaluation of AMF effects. Furthermore, we demonstrate the capacity of the ionome to reveal host genotype-specific variation in the impact of AMF on plant nutrition.
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Affiliation(s)
- Meng Li
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA
| | - Sergio Perez-Limón
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA
| | - M Rosario Ramírez-Flores
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Benjamín Barrales-Gamez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
- Postgrado en Recursos Genéticos y Productividad-Genética, Campus Montecillo, Colegio de Postgraduados, Montecillo, Texcoco, Edo. de México, 56230, México
| | - Marco Antonio Meraz-Mercado
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Gregory Ziegler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA.
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31
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Lanfranco L, Bonfante P. Lessons from arbuscular mycorrhizal fungal genomes. Curr Opin Microbiol 2023; 75:102357. [PMID: 37419003 DOI: 10.1016/j.mib.2023.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) have accompanied the majority of land plants since their evolution in the Devonian period with a symbiotic alliance centered on nutrient exchanges. The exploration of AMF genomes is providing clues to explain major questions about their biology, evolution, and ecology. The dynamics of nuclei across the fungal life cycle, the abundance of transposable elements, and the epigenome landscape are emerging as sources of intraspecific variability, which can be especially important in organisms with no or rare sexual reproduction such as AMF. These features have been hypothesized to support AMF adaptability to a wide host range and to environmental changes. New insights on plant-fungus communication and on the iconic function of phosphate transport were also recently obtained that overall contribute to a better understanding of this ancient and fascinating symbiosis.
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Affiliation(s)
- Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy.
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
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32
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Djotan AKG, Matsushita N, Fukuda K. Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands. Microb Ecol 2023; 86:2133-2146. [PMID: 37115261 PMCID: PMC10497666 DOI: 10.1007/s00248-023-02223-9] [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: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.
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Affiliation(s)
- Akotchiffor Kevin Geoffroy Djotan
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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33
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Smith AH, Bogar LM, Moeller HV. Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi. FEMS Microbiol Ecol 2023; 99:fiad108. [PMID: 37697652 PMCID: PMC10516346 DOI: 10.1093/femsec/fiad108] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023] Open
Abstract
Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.
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Affiliation(s)
- Alexander H Smith
- Department of Integrative Biology, University of Colorado, Denver Auraria Campus Science Building 1150 12th St, Denver CO 80204, USA
| | - Laura M Bogar
- Department of Plant Biology, University of California, Davis, 605 Hutchison Dr Green Hall rm 1002 Davis CA 95616-5720, USA
| | - Holly V Moeller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara CA 93106-9620, USA
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34
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Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Commun Biol 2023; 6:948. [PMID: 37723238 PMCID: PMC10507103 DOI: 10.1038/s42003-023-05299-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023] Open
Abstract
Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
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Affiliation(s)
- Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Julian A Liber
- Department of Biology, Duke University, Durham, NC, 27704, USA
| | - Abigail E Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Alan Kuo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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35
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Zhang Q, Wang S, Xie Q, Xia Y, Lu L, Wang M, Wang G, Long S, Cai Y, Xu L, Wang E, Jiang Y. Control of arbuscule development by a transcriptional negative feedback loop in Medicago. Nat Commun 2023; 14:5743. [PMID: 37717076 PMCID: PMC10505183 DOI: 10.1038/s41467-023-41493-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/06/2023] [Indexed: 09/18/2023] Open
Abstract
Most terrestrial plants establish a symbiosis with arbuscular mycorrhizal fungi (AMF), which provide them with lipids and sugars in exchange for phosphorus and nitrogen. Nutrient exchange must be dynamically controlled to maintain a mutually beneficial relationship between the two symbiotic partners. The WRI5a and its homologues play a conserved role in lipid supply to AMF. Here, we demonstrate that the AP2/ERF transcription factor MtERM1 binds directly to AW-box and AW-box-like cis-elements in the promoters of MtSTR2 and MtSTR, which are required for host lipid efflux and arbuscule development. The EAR domain-containing transcription factor MtERF12 is also directly activated by MtERM1/MtWRI5a to negatively regulate arbuscule development, and the TOPLESS co-repressor is further recruited by MtERF12 through EAR motif to oppose MtERM1/MtWRI5a function, thereby suppressing arbuscule development. We therefore reveal an ERM1/WRI5a-ERF12-TOPLESS negative feedback loop that enables plants to flexibly control nutrient exchange and ensure a mutually beneficial symbiosis.
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Affiliation(s)
- Qiang Zhang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Shuangshuang Wang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Qiujin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yuanjun Xia
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Lei Lu
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Siyu Long
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Yunfei Cai
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Ling Xu
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Yina Jiang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China.
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36
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Sevanto S, Gehring CA, Ryan MG, Patterson A, Losko AS, Vogel SC, Carter KR, Dickman LT, Espy MA, Kuske CR. Benefits of symbiotic ectomycorrhizal fungi to plant water relations depend on plant genotype in pinyon pine. Sci Rep 2023; 13:14424. [PMID: 37660169 PMCID: PMC10475095 DOI: 10.1038/s41598-023-41191-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023] Open
Abstract
Rhizosphere microbes, such as root-associated fungi, can improve plant access to soil resources, affecting plant health, productivity, and stress tolerance. While mycorrhizal associations are ubiquitous, plant-microbe interactions can be species specific. Here we show that the specificity of the effects of microbial symbionts on plant function can go beyond species level: colonization of roots by ectomycorrhizal fungi (EMF) of the genus Geopora has opposite effects on water uptake, and stomatal control of desiccation in drought tolerant and intolerant genotypes of pinyon pine (Pinus edulis Engelm.). These results demonstrate, for the first time, that microorganisms can have significant and opposite effects on important plant functional traits like stomatal control of desiccation that are associated with differential mortality and growth in nature. They also highlight that appropriate pairing of plant genotypes and microbial associates will be important for mitigating climate change impacts on vegetation.
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Affiliation(s)
- Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, PO Box 1663, Los Alamos, NM, 87545, USA.
| | - Catherine A Gehring
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Max G Ryan
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, PO Box 1663, Los Alamos, NM, 87545, USA
- Integral Ecology Group, Duncan, BC, V9L 6H1, Canada
| | - Adair Patterson
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Adrian S Losko
- Material Sciences and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Forschungs-Neutronenquelle Heinz Maier-Leibnitz, 85748, Garching, Germany
| | - Sven C Vogel
- Material Sciences and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Kelsey R Carter
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, PO Box 1663, Los Alamos, NM, 87545, USA
| | - L Turin Dickman
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, PO Box 1663, Los Alamos, NM, 87545, USA
| | - Michelle A Espy
- Engineering Technology and Design Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Cheryl R Kuske
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Silva AMM, Feiler HP, Lacerda-Júnior GV, Fernandes-Júnior PI, de Tarso Aidar S, de Araújo VAVP, Matteoli FP, de Araújo Pereira AP, de Melo IS, Cardoso EJBN. Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest. Braz J Microbiol 2023; 54:1955-1967. [PMID: 37410249 PMCID: PMC10485230 DOI: 10.1007/s42770-023-01058-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Arbuscular mycorrhizal fungi form symbiotic associations with 80-90% of all known plants, allowing the fungi to acquire plant-synthesized carbon, and confer an increased capacity for nutrient uptake by plants, improving tolerance to abiotic and biotic stresses. We aimed at characterizing the mycorrhizal community in the rhizosphere of Neoglaziovia variegata (so-called `caroa`) and Tripogonella spicata (so-called resurrection plant), using high-throughput sequencing of the partial 18S rRNA gene. Both plants are currently undergoing a bioprospecting program to find microbes with the potential of helping plants tolerate water stress. Sampling was carried out in the Caatinga biome, a neotropical dry forest, located in northeastern Brazil. Illumina MiSeq sequencing of 37 rhizosphere samples (19 for N. variegata and 18 for T. spicata) revealed a distinct mycorrhizal community between the studied plants. According to alpha diversity analyses, T. spicata showed the highest richness and diversity based on the Observed ASVs and the Shannon index, respectively. On the other hand, N. variegata showed higher modularity of the mycorrhizal network compared to T. spicata. The four most abundant genera found (higher than 10%) were Glomus, Gigaspora, Acaulospora, and Scutellospora, with Glomus being the most abundant in both plants. Nonetheless, Gigaspora, Diversispora, and Ambispora were found only in the rhizosphere of N. variegata, whilst Scutellospora, Paraglomus, and Archaeospora were exclusive to the rhizosphere of T. spicata. Therefore, the community of arbuscular mycorrhizal fungi of the rhizosphere of each plant encompasses a unique composition, structure and modularity, which can differentially assist them in the hostile environment.
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Affiliation(s)
- Antonio Marcos Miranda Silva
- “Luiz de Queiroz” College of Agriculture, Soil Science Department, University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | | | | | | | - Saulo de Tarso Aidar
- Brazilian Agricultural Research Corporation, Embrapa Semiárido, Petrolina, , Pernambuco 56302-970 Brazil
| | | | - Filipe Pereira Matteoli
- Faculty of Sciences, Department of Biological Sciences, Laboratory of Microbial Bioinformatics, São Paulo State University, Bauru, 17033-360 Brazil
| | | | - Itamar Soares de Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, São Paulo 13918-110 Brazil
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Luo J, Walsh E, Groben G, Justiniano B, Zhang N. Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem. Mycologia 2023; 115:602-613. [PMID: 37561445 DOI: 10.1080/00275514.2023.2234269] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/05/2023] [Indexed: 08/11/2023]
Abstract
Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.
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Affiliation(s)
- Jing Luo
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Emily Walsh
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Glen Groben
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Brandon Justiniano
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, New Jersey, 08901
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Ezawa T, Silvestri A, Maruyama H, Tawaraya K, Suzuki M, Duan Y, Turina M, Lanfranco L. Structurally distinct mitoviruses: are they an ancestral lineage of the Mitoviridae exclusive to arbuscular mycorrhizal fungi (Glomeromycotina)? mBio 2023; 14:e0024023. [PMID: 37162347 PMCID: PMC10470734 DOI: 10.1128/mbio.00240-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/10/2023] [Indexed: 05/11/2023] Open
Abstract
Mitoviruses in the family Mitoviridae are the mitochondria-replicating "naked RNA viruses" with genomes encoding only the replicase RNA-dependent RNA polymerase (RdRp) and prevalent across fungi, plants, and invertebrates. Arbuscular mycorrhizal fungi in the subphylum Glomeromycotina are obligate plant symbionts that deliver water and nutrients to the host. We discovered distinct mitoviruses in glomeromycotinian fungi, namely "large duamitovirus," encoding unusually large RdRp with a unique N-terminal motif that is endogenized in some host genomes. More than 400 viral sequences similar to the large duamitoviruses are present in metatranscriptome databases. They are globally distributed in soil ecosystems, consistent with the cosmopolitan distribution of glomeromycotinian fungi, and formed the most basal clade of the Mitoviridae in phylogenetic analysis. Given that glomeromycotinian fungi are the only confirmed hosts of these viruses, we propose the hypothesis that large duamitoviruses are the most ancestral lineage of the Mitoviridae that have been maintained exclusively in glomeromycotinian fungi.
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Affiliation(s)
- Tatsuhiro Ezawa
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Alessandro Silvestri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Hayato Maruyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Mei Suzuki
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yu Duan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Massimo Turina
- Institute for Sustainable Plant Protection–CNR Torino, Torino, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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López-Angulo J, Matesanz S, Illuminati A, Pescador DS, Sánchez AM, Pías B, Chacón-Labella J, de la Cruz M, Escudero A. Ecological drivers of fine-scale distribution of arbuscular mycorrhizal fungi in a semiarid Mediterranean scrubland. Ann Bot 2023; 131:1107-1119. [PMID: 36976581 PMCID: PMC10457037 DOI: 10.1093/aob/mcad050] [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: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals by the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and below-ground plant community attributes (i.e. diversity and composition), soil heterogeneity and spatial covariates on the spatial structure of the AM fungal communities in a semiarid Mediterranean scrubland. Furthermore, we evaluated how the phylogenetic relatedness of both plants and AM fungi shapes these symbiotic relationships. METHODS We characterized the composition and diversity of AM fungal and plant communities in a dry Mediterranean scrubland taxonomically and phylogenetically, using DNA metabarcoding and a spatially explicit sampling design at the plant neighbourhood scale. KEY RESULTS The above- and below-ground plant community attributes, soil physicochemical properties and spatial variables explained unique fractions of AM fungal diversity and composition. Mainly, variations in plant composition affected the AM fungal composition and diversity. Our results also showed that particular AM fungal taxa tended to be associated with closely related plant species, suggesting the existence of a phylogenetic signal. Although soil texture, fertility and pH affected AM fungal community assembly, spatial factors had a greater influence on AM fungal community composition and diversity than soil physicochemical properties. CONCLUSIONS Our results highlight that the more easily accessible above-ground vegetation is a reliable indicator of the linkages between plant roots and AM fungi. We also emphasize the importance of soil physicochemical properties in addition to below-ground plant information, while accounting for the phylogenetic relationships of both plants and fungi, because these factors improve our ability to predict the relationships between AM fungal and plant communities.
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Affiliation(s)
- Jesús López-Angulo
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH), 8092 Zurich, Switzerland
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Angela Illuminati
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - David S Pescador
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ana M Sánchez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Beatriz Pías
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Marcelino de la Cruz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
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Hiiesalu I, Schweichhart J, Angel R, Davison J, Doležal J, Kopecký M, Macek M, Řehakova K. Plant-symbiotic fungal diversity tracks variation in vegetation and the abiotic environment along an extended elevational gradient in the Himalayas. FEMS Microbiol Ecol 2023; 99:fiad092. [PMID: 37562924 DOI: 10.1093/femsec/fiad092] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/30/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi can benefit plants under environmental stress, and influence plant adaptation to warmer climates. However, very little is known about the ecology of these fungi in alpine environments. We sampled plant roots along a large fraction (1941-6150 m asl (above sea level)) of the longest terrestrial elevational gradient on Earth and used DNA metabarcoding to identify AM fungi. We hypothesized that AM fungal alpha and beta diversity decreases with increasing elevation, and that different vegetation types comprise dissimilar communities, with cultured (putatively ruderal) taxa increasingly represented at high elevations. We found that the alpha diversity of AM fungal communities declined linearly with elevation, whereas within-site taxon turnover (beta diversity) was unimodally related to elevation. The composition of AM fungal communities differed between vegetation types and was influenced by elevation, mean annual temperature, and precipitation. In general, Glomeraceae taxa dominated at all elevations and vegetation types; however, higher elevations were associated with increased presence of Acaulosporaceae, Ambisporaceae, and Claroideoglomeraceae. Contrary to our expectation, the proportion of cultured AM fungal taxa in communities decreased with elevation. These results suggest that, in this system, climate-induced shifts in habitat conditions may facilitate more diverse AM fungal communities at higher elevations but could also favour ruderal taxa.
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Affiliation(s)
- Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50 409 Tartu, Estonia
| | - Johannes Schweichhart
- Biology Centre of the CAS, Institute of Soil Biology and Biochemistry, Na Sádkách 702/7 , 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Roey Angel
- Biology Centre of the CAS, Institute of Soil Biology and Biochemistry, Na Sádkách 702/7 , 370 05 České Budějovice, Czech Republic
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50 409 Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany of the CAS, Dukelská 135, 379 01 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Martin Kopecký
- Institute of Botany of the CAS, Zámek 1, 252 43 Průhonice, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Praha 6, Czech Republic
| | - Martin Macek
- Institute of Botany of the CAS, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Klára Řehakova
- Biology Centre of the CAS, Institute of Hydrobiology, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
- Institute of Botany of the CAS, Dukelská 135, 379 01 Třeboň, Czech Republic
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Behnke-Borowczyk J, Korzeniewicz R, Łukowski A, Baranowska M, Jagiełło R, Bułaj B, Hauke-Kowalska M, Szmyt J, Behnke JM, Robakowski P, Kowalkowski W. Variability of Functional Groups of Rhizosphere Fungi of Norway Spruce ( Picea abies (L.) H.Karst.) in the Boreal Range: The Wigry National Park, Poland. Int J Mol Sci 2023; 24:12628. [PMID: 37628809 PMCID: PMC10454689 DOI: 10.3390/ijms241612628] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plants. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing. Saprotrophs dominated in the studied rhizospheres, but their percentage share decreased with the age of the development group (for 51.91 from 43.13%). However, in the case of mycorrhizal fungi, an opposite trend was observed (16.96-26.75%). The most numerous genera were: saprotrophic Aspergillus (2.54-3.83%), Penicillium (6.47-12.86%), Pyrenochaeta (1.39-11.78%), pathogenic Curvularia (0.53-4.39%), and mycorrhizal Cortinarius (1.80-5.46%), Pseudotomentella (2.94-5.64%) and Tomentella (4.54-15.94%). The species composition of rhizosphere fungal communities was favorable for the regeneration of natural spruce and the development of multi-generational Norway spruce stands. The ratio of the abundance of saprotrophic and mycorrhizal fungi to the abundance of pathogens was high and promising for the durability of the large proportion of spruce in the Wigry National Park and for forest ecosystems in general.
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Affiliation(s)
- Jolanta Behnke-Borowczyk
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Robert Korzeniewicz
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Adrian Łukowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Marlena Baranowska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Radosław Jagiełło
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Bartosz Bułaj
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Maria Hauke-Kowalska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Janusz Szmyt
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Jerzy M. Behnke
- School of Life Sciences, University Park Nottingham, Nottingham NG7 2RD, UK;
| | - Piotr Robakowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Wojciech Kowalkowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
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Braga JGB, de Novais CB, Diniz PP, da Silva Aragão OO, Saggin Júnior OJ, da Conceição Jesus E. Association of mycoheterotrophic Gentianaceae with specific Glomus lineages. Mycorrhiza 2023; 33:249-256. [PMID: 37450045 DOI: 10.1007/s00572-023-01121-9] [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: 03/26/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Some plant species took an alternative evolutionary pathway in which they lost their photosynthetic capacity to depend exclusively on carbon supplied by arbuscular mycorrhizal fungi (AMF) in an association called mycoheterotrophy. Among them is Voyriella parviflora, a species of the family Gentianaceae, which is found in tropical regions such as the Amazon basin. Here, we assessed the identity of AMF symbionts associated with this species. DNA was isolated from eight Gentianaceae specimens and from litter and surrounding roots of photosynthetic plants. The atp1 gene was amplified by Sanger sequencing to determine the taxonomic affiliation of the mycoheterotrophic plants. A 280 bp region of the 18S rRNA gene of AMF was amplified with primers NS31/AML2 by high-throughput sequencing. The mycoheterotrophic specimens were assigned to V. parviflora with a bootstrap support of 72%. Glomus was the most abundant AMF genus, both in the mycoheterotrophic plants and in the litter and roots of photosynthetic plants. In addition, a few Glomus genotypes were abundantly enriched in the mycoheterotrophic plants, with only a few specimens colonized by Gigaspora, Acaulospora, and Scutellospora in a low proportion. These genotypes formed a cluster within a larger clade, suggesting that V. parviflora shows a preferential association with a narrow Glomus lineage which is not phylogenetically close to a previously identified V. parviflora's associated lineage. Furthermore, detecting fungi from other families suggests that V. parviflora is colonized by other genera, although with low frequency. These findings provide new insights into the association between AMF and mycoheterotrophic species and highlight the importance of considering trap culture-independent approaches in understanding this symbiosis.
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Affiliation(s)
| | - Cândido Barreto de Novais
- Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropedica, Rio de Janeiro, 23890-000, Brazil
- Scheffer & Cia, Sapezal, Mato Grosso, 78365-000, Brazil
| | | | - Osnar Obede da Silva Aragão
- Universidade Federal de Lavras (UFLA), Lavras, Minas Gerais, Brazil, 37200-900
- Instituto Federal do Pará, Campus Breves, Breves, Pará, 68800-000, Brazil
| | | | - Ederson da Conceição Jesus
- Universidade Federal de Lavras (UFLA), Lavras, Minas Gerais, Brazil, 37200-900.
- Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropedica, Rio de Janeiro, 23890-000, Brazil.
- Embrapa Agrobiologia, Seropédica, Rio de Janeiro, 23891-000, Brazil.
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44
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Manley BF, Lotharukpong JS, Barrera-Redondo J, Llewellyn T, Yildirir G, Sperschneider J, Corradi N, Paszkowski U, Miska EA, Dallaire A. A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3 (Bethesda) 2023; 13:jkad077. [PMID: 36999556 PMCID: PMC10234402 DOI: 10.1093/g3journal/jkad077] [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: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 06/02/2023]
Abstract
The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle.
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Affiliation(s)
- Bethan F Manley
- SPUN|Society for the Protection of Underground Networks, 3500 South DuPont Highway, Suite EI-101, Dover, DE 19901, USA
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Jaruwatana S Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Theo Llewellyn
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Jana Sperschneider
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Uta Paszkowski
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge CB3 0LE, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexandra Dallaire
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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45
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van Galen LG, Orlovich DA, Lord JM, Nilsen AR, Dutoit L, Larcombe MJ. Correlated evolution in an ectomycorrhizal host-symbiont system. New Phytol 2023; 238:1215-1229. [PMID: 36751898 DOI: 10.1111/nph.18802] [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: 11/06/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.
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Affiliation(s)
- Laura G van Galen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - David A Orlovich
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Andy R Nilsen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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46
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Singavarapu B, Du J, Beugnon R, Cesarz S, Eisenhauer N, Xue K, Wang Y, Bruelheide H, Wubet T. Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity. Microbiol Spectr 2023; 11:e0457822. [PMID: 36951585 PMCID: PMC10111882 DOI: 10.1128/spectrum.04578-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/11/2023] [Indexed: 03/24/2023] Open
Abstract
Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Jianqing Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources, Chinese Academy of Sciences, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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47
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Sahin E, Ozbey Saridogan BG, Keskin E, Akata I. Identification and complete genome sequencing of a novel betapartitivirus naturally infecting the mycorrhizal desert truffle Terfezia claveryi. Virus Genes 2023; 59:254-259. [PMID: 36735175 DOI: 10.1007/s11262-023-01972-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Viruses that naturally infect fungal species and capable of establishing mycorrhizae are largely unknown. In this study, we identified and characterized a new partitivirus inhabiting the ascomycete, mycorrhizal desert truffle species Terfezia claveryi, and named it "Terfezia claveryi partitivirus 1" (TcPV1). The entire genome of TcPV1, sequenced by both high throughput sequencing of the total dsRNA extracts and by Sanger sequencing of the RLM-RACE PCR products comprised two dsRNA segments of 2404 bp and 2374 bp, respectively. Both dsRNA genome segments harbored a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. The BLASTp search of the RdRp and CP sequences revealed the highest sequence identities (41.92% and 24.13% identity, respectively) to those of Bipolaris maydis partitivirus 2 and Plasmopara viticola lesion associated partitivirus 5. Molecular phylogenetic analyses of the RdRp sequence showed that TcPV1 fall within a clade composed entirely of members of the genus Betapartitivirus, belonging to the family Partitiviridae. In light of this molecular evidence, TcPV1 is a new member of the genus Betapartitivirus. This is the first report of a new partitivirus hosted by the ascomycete, mycorrhizal fungus T. claveryi.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
| | | | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture, Department of Fisheries and Aquaculture, Ankara University, Dışkapı, 06110, Ankara, Turkey
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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48
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Wang S, Xie X, Che X, Lai W, Ren Y, Fan X, Hu W, Tang M, Chen H. Host- and virus-induced gene silencing of HOG1-MAPK cascade genes in Rhizophagus irregularis inhibit arbuscule development and reduce resistance of plants to drought stress. Plant Biotechnol J 2023; 21:866-883. [PMID: 36609693 PMCID: PMC10037146 DOI: 10.1111/pbi.14006] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 11/18/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi can form beneficial associations with the most terrestrial vascular plant species. AM fungi not only facilitate plant nutrient acquisition but also enhance plant tolerance to various environmental stresses such as drought stress. However, the molecular mechanisms by which AM fungal mitogen-activated protein kinase (MAPK) cascades mediate the host adaptation to drought stimulus remains to be investigated. Recently, many studies have shown that virus-induced gene silencing (VIGS) and host-induced gene silencing (HIGS) strategies are used for functional studies of AM fungi. Here, we identify the three HOG1 (High Osmolarity Glycerol 1)-MAPK cascade genes RiSte11, RiPbs2 and RiHog1 from Rhizophagus irregularis. The expression levels of the three HOG1-MAPK genes are significantly increased in mycorrhizal roots of the plant Astragalus sinicus under severe drought stress. RiHog1 protein was predominantly localized in the nucleus of yeast in response to 1 M sorbitol treatment, and RiPbs2 interacts with RiSte11 or RiHog1 directly by pull-down assay. Importantly, VIGS or HIGS of RiSte11, RiPbs2 or RiHog1 hampers arbuscule development and decreases relative water content in plants during AM symbiosis. Moreover, silencing of HOG1-MAPK cascade genes led to the decreased expression of drought-resistant genes (RiAQPs, RiTPSs, RiNTH1 and Ri14-3-3) in the AM fungal symbiont in response to drought stress. Taken together, this study demonstrates that VIGS or HIGS of AM fungal HOG1-MAPK cascade inhibits arbuscule development and expression of AM fungal drought-resistant genes under drought stress.
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Affiliation(s)
- Sijia Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xianrong Che
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Wenzhen Lai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Ying Ren
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
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49
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Maillard F, Kohler A, Morin E, Hossann C, Miyauchi S, Ziegler-Devin I, Gérant D, Angeli N, Lipzen A, Keymanesh K, Johnson J, Barry K, Grigoriev IV, Martin FM, Buée M. Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. New Phytol 2023; 238:845-858. [PMID: 36702619 DOI: 10.1111/nph.18773] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire 15 N from 15 N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.
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Affiliation(s)
- François Maillard
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Christian Hossann
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | | | - Dominique Gérant
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, 54000, Nancy, France
| | - Nicolas Angeli
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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50
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Liu H, Jacquemyn H, Yu S, Chen W, He X, Huang Y. Mycorrhizal diversity and community composition in co-occurring Cypripedium species. Mycorrhiza 2023; 33:107-118. [PMID: 36396734 DOI: 10.1007/s00572-022-01095-0] [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: 05/29/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Orchids commonly rely on mycorrhizal fungi to obtain the necessary resources for seed germination and growth. Whereas most photosynthetic orchids typically associate with so-called rhizoctonia fungi to complete their life cycle, there is increasing evidence that other fungi may be involved as well and that the mycorrhizal communities associated with orchids may be more diverse. Coexisting orchid species also tend to associate with different fungi to reduce competition for similar resources and to increase long-term population viability. However, few studies have related the mycorrhizal communities in the rhizosphere to communities found in the roots of closely related coexisting orchid species. In this study, we used high-throughput sequencing to investigate the diversity and community composition of orchid mycorrhizal fungi in the roots and the rhizosphere of four Cypripedium species growing in forests in Northeast China. The results showed that the investigated Cypripedium species associated with a wide variety of fungi including members of Tulasnellaceae, Psathyrellaceae, and Herpotrichiellaceae, whereas members of Russulaceae, Cortinariaceae, Thelephoraceae, and Herpotrichiellaceae showed high abundance in rhizosphere soils. The diversity of fungi detected in the rhizosphere soil was much higher than that in the roots. The observed variation in fungal communities in Cypripedium roots was not related to forest site or orchid species. On the other hand, variation in mycorrhizal communities of rhizosphere soil was significantly related to sampling site. These results indicate that orchid mycorrhizal communities in the rhizosphere display considerable variation among sites and that orchids use only a subset of the locally available fungi. Future studies focusing on the fine-scale spatial distribution of orchid mycorrhizal fungi and more detailed assessments of local environmental conditions will provide novel insights into the mechanisms explaining variation of fungal communities in both orchid roots and the rhizosphere.
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Affiliation(s)
- Huanchu Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiangxi, 332900, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Shuai Yu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Wei Chen
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China.
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China.
| | - Xingyuan He
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yanqing Huang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
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