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Zhang K, Wang H, Tappero R, Bhatnagar JM, Vilgalys R, Barry K, Keymanesh K, Tejomurthula S, Grigoriev IV, Kew WR, Eder EK, Nicora CD, Liao HL. Ectomycorrhizal fungi enhance pine growth by stimulating iron-dependent mechanisms with trade-offs in symbiotic performance. THE NEW PHYTOLOGIST 2024; 242:1645-1660. [PMID: 38062903 DOI: 10.1111/nph.19449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/13/2023] [Indexed: 04/26/2024]
Abstract
Iron (Fe) is crucial for metabolic functions of living organisms. Plants access occluded Fe through interactions with rhizosphere microorganisms and symbionts. Yet, the interplay between Fe addition and plant-mycorrhizal interactions, especially the molecular mechanisms underlying mycorrhiza-assisted Fe processing in plants, remains largely unexplored. We conducted mesocosms in Pinus plants inoculated with different ectomycorrhizal fungi (EMF) Suillus species under conditions with and without Fe coatings. Meta-transcriptomic, biogeochemical, and X-ray fluorescence imaging analyses were applied to investigate early-stage mycorrhizal roots. While Fe addition promoted Pinus growth, it concurrently reduced mycorrhiza formation rate, symbiosis-related metabolites in plant roots, and aboveground plant carbon and macronutrient content. This suggested potential trade-offs between Fe-enhanced plant growth and symbiotic performance. However, the extent of this trade-off may depend on interactions between host plants and EMF species. Interestingly, dual EMF species were more effective at facilitating plant Fe uptake by inducing diverse Fe-related functions than single-EMF species. This subsequently triggered various Fe-dependent physiological and biochemical processes in Pinus roots, significantly contributing to Pinus growth. However, this resulted in a greater carbon allocation to roots, relatively reducing the aboveground plant carbon content. Our study offers critical insights into how EMF communities rebalance benefits of Fe-induced effects on symbiotic partners.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan Tappero
- Brookhaven National Laboratory, NSLS-II, Upton, NY, 11973, USA
| | | | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - William R Kew
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Elizabeth K Eder
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, 32611, USA
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2
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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. THE NEW PHYTOLOGIST 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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Xie QY, Kuo LY, Chang CC, Lin CJ, Wang WH, Chen KH. Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum. AMERICAN JOURNAL OF BOTANY 2024:e16319. [PMID: 38641926 DOI: 10.1002/ajb2.16319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/21/2024]
Abstract
PREMISE Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs. METHODS Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA. RESULTS Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves. CONCLUSIONS Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.
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Affiliation(s)
- Qiao-Yi Xie
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing-Hua University, Hsinchu, Taiwan
| | - Chiung-Chih Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Jung Lin
- Fushan Research Center, Taiwan Forestry Research Institute, Yilan, Taiwan
| | - Wen-Hong Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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4
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Plett JM, Wojtalewicz D, Plett KL, Collin S, Kohler A, Jacob C, Martin F. Sesquiterpenes of the ectomycorrhizal fungus Pisolithus microcarpus alter root growth and promote host colonization. MYCORRHIZA 2024; 34:69-84. [PMID: 38441669 PMCID: PMC10998793 DOI: 10.1007/s00572-024-01137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/01/2024] [Indexed: 04/07/2024]
Abstract
Trees form symbioses with ectomycorrhizal (ECM) fungi, maintained in part through mutual benefit to both organisms. Our understanding of the signaling events leading to the successful interaction between the two partners requires further study. This is especially true for understanding the role of volatile signals produced by ECM fungi. Terpenoids are a predominant class of volatiles produced by ECM fungi. While several ECM genomes are enriched in the enzymes responsible for the production of these volatiles (i.e., terpene synthases (TPSs)) when compared to other fungi, we have limited understanding of the biochemical products associated with each enzyme and the physiological impact of specific terpenes on plant growth. Using a combination of phylogenetic analyses, RNA sequencing, and functional characterization of five TPSs from two distantly related ECM fungi (Laccaria bicolor and Pisolithus microcarpus), we investigated the role of these secondary metabolites during the establishment of symbiosis. We found that despite phylogenetic divergence, these TPSs produced very similar terpene profiles. We focused on the role of P. microcarpus terpenes and found that the fungus expressed a diverse array of mono-, di-, and sesquiterpenes prior to contact with the host. However, these metabolites were repressed following physical contact with the host Eucalyptus grandis. Exposure of E. grandis to heterologously produced terpenes (enriched primarily in γ -cadinene) led to a reduction in the root growth rate and an increase in P. microcarpus-colonized root tips. These results support a very early putative role of fungal-produced terpenes in the establishment of symbiosis between mycorrhizal fungi and their hosts.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
| | - Dominika Wojtalewicz
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, 2568, Australia
| | - Sabrina Collin
- Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | | | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
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5
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Rose BD, Dellinger MA, Larmour CP, Polishook MI, Higuita-Aguirre MI, Dutta S, Cook RL, Zimmermann SD, Garcia K. The ectomycorrhizal fungus Paxillus ammoniavirescens influences the effects of salinity on loblolly pine in response to potassium availability. Environ Microbiol 2024; 26:e16597. [PMID: 38450872 DOI: 10.1111/1462-2920.16597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Salinity is an increasing problem in coastal areas affected by saltwater intrusion, with deleterious effects on tree health and forest growth. Ectomycorrhizal (ECM) fungi may improve the salinity tolerance of host trees, but the impact of external potassium (K+ ) availability on these effects is still unclear. Here, we performed several experiments with the ECM fungus Paxillus ammoniavirescens and loblolly pine (Pinus taeda L.) in axenic and symbiotic conditions at limited or sufficient K+ and increasing sodium (Na+ ) concentrations. Growth rate, biomass, nutrient content, and K+ transporter expression levels were recorded for the fungus, and the colonization rate, root development parameters, biomass, and shoot nutrient accumulation were determined for mycorrhizal and non-mycorrhizal plants. P. ammoniavirescens was tolerant to high salinity, although growth and nutrient concentrations varied with K+ availability and increasing Na+ exposure. While loblolly pine root growth and development decreased with increasing salinity, ECM colonization was unaffected by pine response to salinity. The mycorrhizal influence on loblolly pine salinity response was strongly dependent on external K+ availability. This study reveals that P. ammoniavirescens can reduce Na+ accumulation of salt-exposed loblolly pine, but this effect depends on external K+ availability.
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Affiliation(s)
- Benjamin D Rose
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Marissa A Dellinger
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Clancy P Larmour
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Mira I Polishook
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Maria I Higuita-Aguirre
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Summi Dutta
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Rachel L Cook
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Sabine D Zimmermann
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
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6
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Zhao P, Gao G, Ding G, Zhang Y, Ren Y. Fungal complexity and stability across afforestation areas in changing desert environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169398. [PMID: 38114026 DOI: 10.1016/j.scitotenv.2023.169398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.
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Affiliation(s)
- Peishan Zhao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ying Zhang
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yue Ren
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
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7
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Harder CB, Hesling E, Botnen SS, Lorberau KE, Dima B, von Bonsdorff-Salminen T, Niskanen T, Jarvis SG, Ouimette A, Hester A, Hobbie EA, Taylor AFS, Kauserud H. Mycena species can be opportunist-generalist plant root invaders. Environ Microbiol 2023; 25:1875-1893. [PMID: 37188366 DOI: 10.1111/1462-2920.16398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13 C/15 N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13 C/15 N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Microbial Ecology, Lund University, Lund, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Emily Hesling
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Kelsey E Lorberau
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
| | | | - Andrew Ouimette
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | | | - Erik A Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- The James Hutton Institute, Aberdeen, UK
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8
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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9
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Labban A, Shibl AA, Calleja ML, Hong PY, Morán XAG. Growth dynamics and transcriptional responses of a Red Sea Prochlorococcus strain to varying temperatures. Environ Microbiol 2022; 25:1007-1021. [PMID: 36567447 DOI: 10.1111/1462-2920.16326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/11/2022] [Indexed: 12/27/2022]
Abstract
Prochlorococcus play a crucial role in the ocean's biogeochemical cycling, but it remains controversial how they will respond to global warming. Here we assessed the response to temperature (22-30°C) of the growth dynamics and gene expression profiles of a Red Sea Prochlorococcus strain (RSP50) in a non-axenic culture. Both the specific growth rate (0.55-0.80 day-1 ) and cell size (0.04-0.07 μm3 ) of Prochlorococcus increased significantly with temperature. The primary production released extracellularly ranged from 20% to 34%, with humic-like fluorescent compounds increasing up to fivefold as Prochlorococcus reached its maximum abundance. At 30°C, genes involved in carbon fixation such as CsoS2 and CsoS3 and photosynthetic electron transport including PTOX were downregulated, suggesting a cellular homeostasis and energy saving mechanism response. In contrast, PTOX was found upregulated at 22°C and 24°C. Similar results were found for transaldolase, related to carbon metabolism, and citrate synthase, an important enzyme in the TCA cycle. Our data suggest that in spite of the currently warm temperatures of the Red Sea, Prochlorococcus can modulate its gene expression profiles to permit growth at temperatures lower than its optimum temperature (28°C) but is unable to cope with temperatures exceeding 30°C.
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Affiliation(s)
- Abbrar Labban
- Marine Science, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.,Environmental Science and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ahmed A Shibl
- Genetic Heritage Group, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Maria Ll Calleja
- Climate Geochemistry Department, Max Plank Institute for Chemistry, Mainz, Germany
| | - Pei-Ying Hong
- Environmental Science and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Xosé Anxelu G Morán
- Marine Science, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO-CSIC), Gijón/Xixón, Spain
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10
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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11
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Leaf Mycobiome and Mycotoxin Profile of Warm-Season Grasses Structured by Plant Species, Geography, and Apparent Black-Stroma Fungal Structure. Appl Environ Microbiol 2022; 88:e0094222. [PMID: 36226941 PMCID: PMC9642016 DOI: 10.1128/aem.00942-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Grasses harbor diverse fungi, including some that produce mycotoxins or other secondary metabolites. Recently, Florida cattle farmers reported cattle illness, while the cattle were grazing on warm-season grass pastures, that was not attributable to common causes, such as nutritional imbalances or nitrate toxicity. To understand correlations between grass mycobiome and mycotoxin production, we investigated the mycobiomes associated with five prominent, perennial forage and weed grasses [Paspalum notatum Flügge, Cynodon dactylon (L.) Pers., Paspalum nicorae Parodi, Sporobolus indicus (L.) R. Br., and Andropogon virginicus (L.)] collected from six Florida pastures actively grazed by livestock. Black fungal stromata of Myriogenospora and Balansia were observed on P. notatum and S. indicus leaves and were investigated. High-throughput amplicon sequencing was applied to delineate leaf mycobiomes. Mycotoxins from P. notatum leaves were inspected using liquid chromatography-mass spectrometry (LC-MS/MS). Grass species, cultivars, and geographic localities interactively affected fungal community assemblies of asymptomatic leaves. Among the grass species, the greatest fungal richness was detected in the weed S. indicus. The black fungal structures of P. notatum leaves were dominated by the genus Myriogenospora, while those of S. indicus were codominated by the genus Balansia and a hypermycoparasitic fungus of the genus Clonostachys. When comparing mycotoxins detected in P. notatum leaves with and without M. atramentosa, emodin, an anthraquinone, was the only compound which was significantly different (P < 0.05). Understanding the leaf mycobiome and the mycotoxins it may produce in warm-season grasses has important implications for how these associations lead to secondary metabolite production and their subsequent impact on animal health. IMPORTANCE The leaf mycobiome of forage grasses can have a major impact on their mycotoxin contents of forage and subsequently affect livestock health. Despite the importance of the cattle industry in warm-climate regions, such as Florida, studies have been primarily limited to temperate forage systems. Our study provides a holistic view of leaf fungi considering epibiotic, endophytic, and hypermycoparasitic associations with five perennial, warm-season forage and weed grasses. We highlight that plant identity and geographic location interactively affect leaf fungal community composition. Yeasts appeared to be an overlooked fungal group in healthy forage mycobiomes. Furthermore, we detected high emodin quantities in the leaves of a widely planted forage species (P. notatum) whenever epibiotic fungi occurred. Our study demonstrated the importance of identifying fungal communities, ecological roles, and secondary metabolites in perennial, warm-season grasses and their potential for interfering with livestock health.
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12
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Erlandson SR, Margis R, Ramirez A, Nguyen N, Lofgren LA, Liao HL, Vilgalys R, Kennedy PG, Peay KG. Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens. THE NEW PHYTOLOGIST 2022; 234:1910-1913. [PMID: 34668199 PMCID: PMC10228522 DOI: 10.1111/nph.17816] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/07/2021] [Indexed: 05/31/2023]
Affiliation(s)
- Sonya R. Erlandson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA
| | - Rogerio Margis
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Allegre, 90040-060, Brazil
| | - Andrea Ramirez
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA
| | - Nhu Nguyen
- Department of Tropical Plants and Soil Sciences, University of Hawai’i at Manoa, Honolulu, HI 96822, USA
| | - Lotus A. Lofgren
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92507, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Peter G. Kennedy
- Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Woods Center for the Environment, Stanford University, Stanford, CA 94305, USA
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13
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Chen K, Xie Q, Chang C, Kuo L. Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11461. [PMID: 35495185 PMCID: PMC9039796 DOI: 10.1002/aps3.11461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 05/13/2023]
Abstract
PREMISE Several ferns and lycophytes produce subterranean gametophytes, including the Ophioglossaceae, Psilotaceae, and some members of the Schizaeaceae, Gleicheniaceae, and Lycopodiaceae. Despite the surge in plant-microbiome research, which has been particularly boosted by high-throughput sequencing techniques, the microbiomes of these inconspicuous fern gametophytes have rarely been examined. The subterranean gametophytes are peculiar due to their achlorophyllous nature, which makes them rely on fungi to obtain nutrients. Furthermore, the factors that shape the fungal communities (mycobiomes) of fern gametophytes have not been examined in depth. METHODS AND RESULTS We present a workflow to study the mycobiome of the achlorophyllous gametophytes of Ophioderma pendulum using a high-throughput metabarcoding approach. Simultaneously, each gametophyte was investigated microscopically to detect fungal structures. Two primer sets of the nuclear ITS sequence targeting general fungi were applied, in addition to a primer set that specifically targets the nuclear small subunit ribosomal rDNA region of arbuscular mycorrhizal fungi. Both the microscopic and metabarcoding approaches revealed many diverse fungi inhabiting a single gametophyte of O. pendulum. DISCUSSION This study provides methodological details and discusses precautions for the mycobiome investigation of achlorophyllous gametophytes. This research is also the first to uncover the mycobiome assembly of an achlorophyllous gametophyte of an epiphytic fern.
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Affiliation(s)
- Ko‐Hsuan Chen
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Qiao‐Yi Xie
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Life Science DepartmentNational Taiwan Normal UniversityTaipeiTaiwan
| | | | - Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing‐Hua UniversityHsinchuTaiwan
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14
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Plett KL, Snijders F, Castañeda-Gómez L, Wong-Bajracharya JWH, Anderson IC, Carrillo Y, Plett JM. Nitrogen fertilization differentially affects the symbiotic capacity of two co-occurring ectomycorrhizal species. Environ Microbiol 2022; 24:309-323. [PMID: 35023254 DOI: 10.1111/1462-2920.15879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022]
Abstract
Forest trees rely on ectomycorrhizal (ECM) fungi to obtain growth-limiting nutrients. While addition of nitrogen (N) has the potential to disrupt these critical relationships, there is conflicting evidence as to the mechanism by which ECM:host mutualism may be affected. We evaluated how N fertilization altered host interactions and gene transcription between Eucalyptus grandis and Pisolithus microcarpus or Pisolithus albus, two closely related ECM species that typically co-occur within the same ecosystem. Our investigation demonstrated species-specific responses to elevated N: P. microcarpus maintained its ability to transport microbially sourced N to its host but had a reduced ability to penetrate into root tissues, while P. albus maintained its colonization ability but reduced delivery of N to its host. Transcriptomic analysis suggests that regulation of different suites of N-transporters may be responsible for these species-specific differences. In addition to N-dependent responses, we were also able to define a conserved 'core' transcriptomic response of Eucalyptus grandis to mycorrhization that was independent of abiotic conditions. Our results demonstrate that even between closely related ECM species, responses to N fertilization can vary considerably, suggesting that a better understanding of the breadth and mechanisms of their responses is needed to support forest ecosystems into the future.
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Affiliation(s)
- Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales, 2568, Australia
| | - Fridtjof Snijders
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Laura Castañeda-Gómez
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Johanna W-H Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales, 2568, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Yolima Carrillo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
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15
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Hill RA, Wong-Bajracharya J, Anwar S, Coles D, Wang M, Lipzen A, Ng V, Grigoriev IV, Martin F, Anderson IC, Cazzonelli CI, Jeffries T, Plett KL, Plett JM. Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus. THE NEW PHYTOLOGIST 2022; 233:966-982. [PMID: 34699614 DOI: 10.1111/nph.17825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
The pathways regulated in ectomycorrhizal (EcM) plant hosts during the establishment of symbiosis are not as well understood when compared to the functional stages of this mutualistic interaction. Our study used the EcM host Eucalyptus grandis to elucidate symbiosis-regulated pathways across the three phases of this interaction. Using a combination of RNA sequencing and metabolomics we studied both stage-specific and core responses of E. grandis during colonization by Pisolithus microcarpus. Using exogenous manipulation of the abscisic acid (ABA), we studied the role of this pathway during symbiosis establishment. Despite the mutualistic nature of this symbiosis, a large number of disease signalling TIR-NBS-LRR genes were induced. The transcriptional regulation in E. grandis was found to be dynamic across colonization with a small core of genes consistently regulated at all stages. Genes associated to the carotenoid/ABA pathway were found within this core and ABA concentrations increased during fungal integration into the root. Supplementation of ABA led to improved accommodation of P. microcarpus into E. grandis roots. The carotenoid pathway is a core response of an EcM host to its symbiont and highlights the need to understand the role of the stress hormone ABA in controlling host-EcM fungal interactions.
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Affiliation(s)
- Richard A Hill
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, NSW, 2568, Australia
| | - Sidra Anwar
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Donovin Coles
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- 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
| | - Francis Martin
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE GrandEst-Nancy, Université de Lorraine, 54280, Champenoux, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Thomas Jeffries
- School of Science, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, NSW, 2568, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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16
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Liao HL, Bonito G, Hameed K, Wu SH, Chen KH, Labbé J, Schadt CW, Tuskan GA, Martin F, Kuo A, Barry K, Grigoriev IV, Vilgalys R. Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi. Front Microbiol 2021; 12:680267. [PMID: 34803937 PMCID: PMC8601753 DOI: 10.3389/fmicb.2021.680267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor's microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus, Populus with Pinus, and Pinus with Pinus. Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus-associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.
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Affiliation(s)
- Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States
- Department of Biology, Duke University, Durham, NC, United States
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Khalid Hameed
- Department of Biology, Duke University, Durham, NC, United States
| | - Steven H. Wu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ko-Hsuan Chen
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Invaio Sciences, Cambridge, MA, United States
| | | | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Francis Martin
- University of Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Champenoux, France
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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17
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Tang N, Lebreton A, Xu W, Dai Y, Yu F, Martin FM. Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius-Pinus Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:714393. [PMID: 34490014 PMCID: PMC8417538 DOI: 10.3389/fpls.2021.714393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Ectomycorrhizal fungi establish a mutualistic symbiosis in roots of most woody plants. The molecular underpinning of ectomycorrhizal development was only explored in a few lineages. Here, we characterized the symbiotic transcriptomes of several milkcap species (Lactarius, Russulales) in association with different pine hosts. A time-course study of changes in gene expression during the development of L. deliciosus-Pinus taeda symbiosis identified 6 to 594 differentially expressed fungal genes at various developmental stages. Up- or down-regulated genes are involved in signaling pathways, nutrient transport, cell wall modifications, and plant defenses. A high number of genes coding for secreted proteases, especially sedolisins, were induced during root colonization. In contrast, only a few genes encoding mycorrhiza-induced small secreted proteins were identified. This feature was confirmed in several other Lactarius species in association with various pines. Further comparison among all these species revealed that each Lactarius species encodes a highly specific symbiotic gene repertoire, a feature possibly related to their host-specificity. This study provides insights on the genetic basis of symbiosis in an ectomycorrhizal order, the Russulales, which was not investigated so far.
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Affiliation(s)
- Nianwu Tang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Wenjun Xu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Centre INRAE-GrandEst Nancy, INRAE, UMR Interactions Arbres/Microorganismes, Université de Lorraine, Champenoux, France
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18
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Runte GC, Smith AH, Moeller HV, Bogar LM. Spheres of Influence: Host Tree Proximity and Soil Chemistry Shape rRNA, but Not DNA, Communities of Symbiotic and Free-Living Soil Fungi in a Mixed Hardwood-Conifer Forest. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.641732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Host and symbiont diversity are inextricably linked across partnerships and ecosystems, with degree of partner reliance governing the strength of this correlation. In many forest soils, symbiotic ectomycorrhizal fungi coexist and compete with free-living saprotrophic fungi, with the outcomes of these interactions shaping resource availability and competitive outcomes for the trees aboveground. Traditional approaches to characterizing these communities rely on DNA sequencing of a ribosomal precursor RNA gene (the internal transcribed spacer region), but directly sequencing the precursor rRNA may provide a more functionally relevant perspective on the potentially active fungal communities. Here, we map ectomycorrhizal and saprotrophic soil fungal communities through a mixed hardwood-conifer forest to assess how above- and belowground diversity linkages compare across these differently adapted guilds. Using highly spatially resolved transects (sampled every 2 m) and well-mapped stands of varying host tree diversity, we sought to understand the relative influence of symbiosis versus environment in predicting fungal diversity measures. Canopy species in this forest included two oaks (Quercus agrifolia and Quercus douglasii) and one pine (Pinus sabiniana). At the scale of our study, spatial turnover in rRNA-based communities was much more predictable from measurable environmental attributes than DNA-based communities. And while turnover of ectomycorrhizal fungi and saprotrophs were predictable by the presence and abundance of different canopy species, they both responded strongly to soil nutrient characteristics, namely pH and nitrogen availability, highlighting the niche overlap of these coexisting guilds and the strong influence of aboveground plants on belowground fungal communities.
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19
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Lofgren LA, Nguyen NH, Vilgalys R, Ruytinx J, Liao HL, Branco S, Kuo A, LaButti K, Lipzen A, Andreopoulos W, Pangilinan J, Riley R, Hundley H, Na H, Barry K, Grigoriev IV, Stajich JE, Kennedy PG. Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. THE NEW PHYTOLOGIST 2021; 230:774-792. [PMID: 33355923 PMCID: PMC7969408 DOI: 10.1111/nph.17160] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Science, University of Hawaii, Manoa, HI, 96822, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Joske Ruytinx
- Research group Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussel, BE1500, Belgium
| | - Hui-Ling Liao
- Department of Soil Microbial Ecology, University of Florida, Quincy, FL, 32351, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, 80204, USA
| | - Alan Kuo
- 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
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hope Hundley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- 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, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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20
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Huang YY, Liang ZC, Lin XZ, He ZG, Ren XY, Li WX, Molnár I. Fungal community diversity and fermentation characteristics in regional varieties of traditional fermentation starters for Hong Qu glutinous rice wine. Food Res Int 2021; 141:110146. [PMID: 33642012 DOI: 10.1016/j.foodres.2021.110146] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/16/2023]
Abstract
Hong Qu glutinous rice wine (HQ wine) is a traditional alcoholic beverage produced in China by fermenting cooked rice using a fermentation starter prepared with the fungus Monascus purpureus. This starter (Hong Qu, HQ) is made empirically by open spontaneous fermentation that is hard to control and standardize, resulting in inconsistent wine quality. This study investigates representative HQ samples from a large geographic region. It explores fungal microbiome compositions, identifies characteristic differences important for the production of various HQ wine styles, and reveals the key fungi responsible for HQ wine fermentation characteristics. The source of the HQ inoculum was found to be the main factor influencing fungal community composition and diversity, followed by processing technology and geographical distribution. Linear discriminant analysis effect size (LEfSe) uncovered 14 genera as potential biomarkers to distinguish regional varieties of HQ. Significant differences were also found in fermentation characteristics such as liquefying power (LP), saccharifying power (SP), fermenting power (FP), total acid content (TA) and liquor-producing power (LPP). The key fungi responsible for LP (5 genera), SP (3 genera), FP (1 genera), LPP (4 genera), and TA (4 genera) were determined using redundancy correlation analysis. Finally, Spearman's correlation analysis indicated that LPP shows a strong positive correlation with FP and LP, while TA displays a strong negative correlation with FP. The results of this study may be utilized to prepare consistently high quality, next-generation HQ by better controlling fungal community structures, and to design fermentation processes for HQ wines with desirable oenological characteristics.
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Affiliation(s)
- Ying-Ying Huang
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China; Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Zhang-Cheng Liang
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China
| | - Xiao-Zi Lin
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China.
| | - Zhi-Gang He
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China.
| | - Xiang-Yun Ren
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China
| | - Wei-Xin Li
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350003, PR China; Fujian Key Laboratory of Agricultural Products (Food) Processing, 350003 Fuzhou, Fujian Province, PR China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.
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21
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Bazzicalupo AL, Ruytinx J, Ke Y, Coninx L, Colpaert JV, Nguyen NH, Vilgalys R, Branco S. Fungal heavy metal adaptation through single nucleotide polymorphisms and copy‐number variation. Mol Ecol 2020; 29:4157-4169. [DOI: 10.1111/mec.15618] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Anna L. Bazzicalupo
- Department of Microbiology and Immunology Montana State University Bozeman MT USA
| | - Joske Ruytinx
- Research Group of Microbiology Department of Bioengineering Sciences Vrije Universiteit Brussel Brussels Belgium
| | - Yi‐Hong Ke
- Biology Department Duke University Durham NC USA
| | - Laura Coninx
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Jan V. Colpaert
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences University of Hawai'i at Mānoa Honolulu HI USA
| | | | - Sara Branco
- Department of Integrative Biology University of Colorado Denver Denver CO USA
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22
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Liang Z, Lin X, He Z, Su H, Li W, Ren X. Amino acid and microbial community dynamics during the fermentation of Hong Qu glutinous rice wine. Food Microbiol 2020; 90:103467. [DOI: 10.1016/j.fm.2020.103467] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/13/2020] [Accepted: 01/19/2020] [Indexed: 01/19/2023]
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23
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Liang Z, Su H, Lin X, He Z, Li W, Deng D. Microbial communities and amino acids during the fermentation of Wuyi Hong Qu Huangjiu. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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24
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Thoen E, Harder CB, Kauserud H, Botnen SS, Vik U, Taylor AFS, Menkis A, Skrede I. In vitro evidence of root colonization suggests ecological versatility in the genus Mycena. THE NEW PHYTOLOGIST 2020; 227:601-612. [PMID: 32171021 DOI: 10.1111/nph.16545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14 C and 32 P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32 P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.
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Affiliation(s)
- Ella Thoen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
- Department of Plant and Soil Science, Texas Tech University, PO Box 42122, Lubbock, TX, 79409, USA
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Unni Vik
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, SE-75007, Uppsala, Sweden
| | - Inger Skrede
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
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25
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Liang ZC, Lin XZ, He ZG, Su H, Li WX, Guo QQ. Comparison of microbial communities and amino acid metabolites in different traditional fermentation starters used during the fermentation of Hong Qu glutinous rice wine. Food Res Int 2020; 136:109329. [PMID: 32846528 DOI: 10.1016/j.foodres.2020.109329] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
Hong Qu glutinous rice wine (HQGRW) is produced from glutinous rice with the addition of the traditional fermentation starter Hong Qu (mainly Gutian Hong Qu and Wuyi Hong Qu) has been added. It is unpalatable and rejected by consumers because the bitter and umami tastes are too high. The objective of this study was to compare the dynamics of the microbial communities and amino acids especially those in the different traditional fermentation starters used during HQGRW fermentation, and elucidate the key microbes responsible for amino acids. Three widely-used types of Hong Qu starters were used which can make different bitterness and umami in our previous studies, namely, black Wuyi Hong Qu (WB), red Wuyi Hong Qu (WR), and Gutian Hong Qu (GT). The living dynamics of fungal and bacterial communities during the fermentation were determined by high-throughput sequencing and rRNA gene sequencing technology for the first time. The content of amino acids in the HQGRW were determined by reverse-phase high-performance liquid chromatography analysis. The results showed that there were differences between fungal communities during the fermentation process in Wuyi Hong Qu and Gutian Hong Qu starters and between bacterial communities during the fermentation process in the three types of starters. The amino acid content of the samples showed an increasing trend in each group. The total amino acids, as well as the bitter, sweet, umami, astringent amino acids, in the GT Hong Qu group increased more slowly during fermentation, as comparerd to those in WB and WR groups. Furthermore, Meyerozyma, Saccharomyces, Bacillus, Rhizopus, Pediococcus, Monascus, and Halomonas were strongly positively correlated with the content of bitter and umami amino acids (|r| > 0.6 with FDR adjusted P < 0.05) by Spearman's correlation analysis. To conclude, these findings may contribute to a better understanding of the bitter and umami amino acid production mechanism during traditional fermentation and helpful in improving the taste of HQGRW.
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Affiliation(s)
- Zhang-Cheng Liang
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China
| | - Xiao-Zi Lin
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China.
| | - Zhi-Gang He
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China.
| | - Hao Su
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China
| | - Wei-Xin Li
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China
| | - Qi-Qi Guo
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China; Fujian Key Laboratory of Agricultural Products (Food) Processing, Fuzhou, Fujian, China
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26
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 397] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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27
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Marcelino VR, Irinyi L, Eden JS, Meyer W, Holmes EC, Sorrell TC. Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions. IMA Fungus 2019; 10:12. [PMID: 32355612 PMCID: PMC7184889 DOI: 10.1186/s43008-019-0012-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse, but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study highlights both the advantages and current challenges in the application of metatranscriptomics in clinical mycology and ecological studies.
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Affiliation(s)
- Vanesa R Marcelino
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145 Australia.,4School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
| | - Laszlo Irinyi
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - John-Sebastian Eden
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Wieland Meyer
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145 Australia.,3Westmead Hospital (Research and Education Network), Westmead, NSW 2145 Australia
| | - Edward C Holmes
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,4School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
| | - Tania C Sorrell
- 1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
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28
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Montesinos-Navarro A, Valiente-Banuet A, Verdú M. Processes underlying the effect of mycorrhizal symbiosis on plant-plant interactions. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Liao HL, Bonito G, Rojas JA, Hameed K, Wu S, Schadt CW, Labbé J, Tuskan GA, Martin F, Grigoriev IV, Vilgalys R. Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:853-864. [PMID: 30699306 DOI: 10.1094/mpmi-05-18-0133-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth.
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Affiliation(s)
- Hui-Ling Liao
- 1 North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, U.S.A
| | - Gregory Bonito
- 2 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - J Alejandro Rojas
- 3 Department of Biology, Duke University, Durham, NC, U.S.A
- 4 Plant Pathology Department, University of Arkansas, 211 PTSC-Fayetteville, AR 72701, U.S.A
| | - Khalid Hameed
- 3 Department of Biology, Duke University, Durham, NC, U.S.A
| | - Steven Wu
- 5 Independent Researcher, Davis, CA, U.S.A
| | - Christopher W Schadt
- 6 Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, U.S.A
| | - Jessy Labbé
- 6 Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, U.S.A
| | - Gerald A Tuskan
- 6 Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, U.S.A
| | - Francis Martin
- 7 INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Igor V Grigoriev
- 8 U.S. Department of Energy Joint Genome Institute and Department of Plant and Microbial Biology, University of California Berkeley, 2800 Mitchell Drive, Walnut Creek, CA 94598, U.S.A
| | - Rytas Vilgalys
- 3 Department of Biology, Duke University, Durham, NC, U.S.A
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30
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Veličkovic D, Liao HL, Vilgalys R, Chu RK, Anderton CR. Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization. JOURNAL OF NATURAL PRODUCTS 2019; 82:1382-1386. [PMID: 31009217 DOI: 10.1021/acs.jnatprod.8b01050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Root alkaloids remain highly unexplored in ectomycorrhizae development studies. By employing ultrahigh mass resolution mass spectrometry imaging techniques, we showed substantial relocation and transformation of piperidine alkaloids in pine root tips in response to Suillus mycorrhization. We imaged, in the time frame of ectomycorrhizae formation, a completely different alkaloid profile in Pinus strobus, where basidiospores of Suillus spraguei induce morphogenesis of symbiotic tissues, than in Pinus taeda, where such interaction fails to induce morphogenesis. On the basis of spatial colocalization studies, we proposed some alternative routes for biosynthesis of these alkaloids that supplement existing literature data.
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Affiliation(s)
- Dušan Veličkovic
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Hui-Ling Liao
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
- North Florida Research and Education Center , University of Florida , 155 Research Road , Quincy , Florida 32351 , United States
| | - Rytas Vilgalys
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
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31
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Hess J, Skrede I, Chaib De Mares M, Hainaut M, Henrissat B, Pringle A. Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. Mol Biol Evol 2018; 35:2786-2804. [PMID: 30239843 PMCID: PMC6231487 DOI: 10.1093/molbev/msy179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
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Affiliation(s)
- Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Maryam Chaib De Mares
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, Madison, WI
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Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes. Appl Environ Microbiol 2018; 84:AEM.01133-18. [PMID: 30097442 DOI: 10.1128/aem.01133-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/04/2018] [Indexed: 11/20/2022] Open
Abstract
Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.
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Mercado-Blanco J, Abrantes I, Barra Caracciolo A, Bevivino A, Ciancio A, Grenni P, Hrynkiewicz K, Kredics L, Proença DN. Belowground Microbiota and the Health of Tree Crops. Front Microbiol 2018; 9:1006. [PMID: 29922245 PMCID: PMC5996133 DOI: 10.3389/fmicb.2018.01006] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.
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Affiliation(s)
- Jesús Mercado-Blanco
- Department of Crop Protection, Agencia Estatal Consejo Superior de Investigaciones Científicas, Institute for Sustainable Agriculture, Córdoba, Spain
| | - Isabel Abrantes
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | | | - Annamaria Bevivino
- Department for Sustainability of Production and Territorial Systems, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Aurelio Ciancio
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy
| | - Paola Grenni
- Water Research Institute (CNR-IRSA), National Research Council, Rome, Italy
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Diogo N. Proença
- Centre for Mechanical Engineering, Materials and Processes (CEMMPRE) and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Chen KH, Liao HL, Arnold AE, Bonito G, Lutzoni F. RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi. THE NEW PHYTOLOGIST 2018; 218:1597-1611. [PMID: 29604236 DOI: 10.1111/nph.15092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/07/2018] [Indexed: 05/15/2023]
Abstract
Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.
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Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Soil and Water Sciences Department, North Florida Research and Education Center, University of Florida, Quincy, FL, 32351, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
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Looney BP, Meidl P, Piatek MJ, Miettinen O, Martin FM, Matheny PB, Labbé JL. Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates. THE NEW PHYTOLOGIST 2018; 218:54-65. [PMID: 29381218 DOI: 10.1111/nph.15001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/13/2017] [Indexed: 05/05/2023]
Abstract
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.
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Affiliation(s)
- Brian P Looney
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
- INRA Université de Lorraine, UMR Interactions Arbres-Microorganismes, Laboratoire d'excellence ARBRE, 54280 Champenoux, France
| | - Peter Meidl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Marek J Piatek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki 00170, Finland
| | - Francis M Martin
- INRA Université de Lorraine, UMR Interactions Arbres-Microorganismes, Laboratoire d'excellence ARBRE, 54280 Champenoux, France
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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Rosenthal LM, Larsson KH, Branco S, Chung JA, Glassman SI, Liao HL, Peay KG, Smith DP, Talbot JM, Taylor JW, Vellinga EC, Vilgalys R, Bruns TD. Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal. Mycologia 2017; 109:115-127. [DOI: 10.1080/00275514.2017.1281677] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lisa M. Rosenthal
- Department of Plant Pathology, University of California Davis, Davis, California 95818
| | | | - Sara Branco
- Ecologie, Systematique et Evolution, Université Paris Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France
| | - Judy A. Chung
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Sydney I. Glassman
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California 94305
| | - Dylan P. Smith
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | | | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Else C. Vellinga
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
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Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS. Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol 2016; 14:760-773. [PMID: 27795567 DOI: 10.1038/nrmicro.2016.149] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
During the diversification of Fungi and the rise of conifer-dominated and angiosperm- dominated forests, mutualistic symbioses developed between certain trees and ectomycorrhizal fungi that enabled these trees to colonize boreal and temperate regions. The evolutionary success of these symbioses is evident from phylogenomic analyses that suggest that ectomycorrhizal fungi have arisen in approximately 60 independent saprotrophic lineages, which has led to the wide range of ectomycorrhizal associations that exist today. In this Review, we discuss recent genomic studies that have revealed the adaptations that seem to be fundamental to the convergent evolution of ectomycorrhizal fungi, including the loss of some metabolic functions and the acquisition of effectors that facilitate mutualistic interactions with host plants. Finally, we consider how these insights can be integrated into a model of the development of ectomycorrhizal symbioses.
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Affiliation(s)
- Francis Martin
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Annegret Kohler
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Claude Murat
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), 54500 Vandoeuvre-lès-Nancy, France
| | - David S Hibbett
- Biology Department, Clark University, Lasry Center for Bioscience, 950 Main Street, Worcester, Massachusetts 01610, USA
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Liao HL, Chen Y, Vilgalys R. Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus. PLoS Genet 2016; 12:e1006348. [PMID: 27736883 PMCID: PMC5065116 DOI: 10.1371/journal.pgen.1006348] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 09/08/2016] [Indexed: 01/19/2023] Open
Abstract
Ectomycorrhizal fungi (EMF) represent one of the major guilds of symbiotic fungi associated with roots of forest trees, where they function to improve plant nutrition and fitness in exchange for plant carbon. Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the genus Suillus, which grows in association with the conifer family Pinaceae. We investigated genetics of EMF host-specificity by cross-inoculating basidiospores of five species of Suillus onto ten species of Pinus, and screened them for their ability to form ectomycorrhizae. Several Suillus spp. including S. granulatus, S. spraguei, and S. americanus readily formed ectomycorrhizae (compatible reaction) with white pine hosts (subgenus Strobus), but were incompatible with other pine hosts (subgenus Pinus). Metatranscriptomic analysis of inoculated roots reveals that plant and fungus each express unique gene sets during incompatible vs. compatible pairings. The Suillus-Pinus metatranscriptomes utilize highly conserved gene regulatory pathways, including fungal G-protein signaling, secretory pathways, leucine-rich repeat and pathogen resistance proteins that are similar to those associated with host-pathogen interactions in other plant-fungal systems. Metatranscriptomic study of the combined Suillus-Pinus transcriptome has provided new insight into mechanisms of adaptation and coevolution of forest trees with their microbial community, and revealed that genetic regulation of ectomycorrhizal symbiosis utilizes universal gene regulatory pathways used by other types of fungal-plant interactions including pathogenic fungal-host interactions. Ectomycorrhizal fungi (EMF) comprise the dominant group of symbiotic fungi associated with plant roots in temperate and boreal forests. We examined host-specificity and gene-expression of five EMF Suillus species that exhibited strong patterns of mycorrhizal compatibility/incompatibility with either white pines (Pinus subg. Strobus) or hard pines (subg. Pinus). Using RNA-Seq, we identified conserved transcriptomic responses associated with compatible versus incompatible Pinus-Suillus species pairings. Comparative metatranscriptomic analysis of compatible vs. incompatible pairings allowed us to identify unique sets of fungal and plant genes associated with symbiont recognition and specificity. Comparativ transcriptomic study of the Suillus-Pinus system provides insight into the core functions involved in ectomycorrhizal symbiosis, and the mechanisms by which host-symbiont pairs recognize one another.
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Affiliation(s)
- Hui-Ling Liao
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Yuan Chen
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Moeller HV, Peay KG. Competition-function tradeoffs in ectomycorrhizal fungi. PeerJ 2016; 4:e2270. [PMID: 27547573 PMCID: PMC4974999 DOI: 10.7717/peerj.2270] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/29/2016] [Indexed: 11/20/2022] Open
Abstract
Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining "high-quality" ectomycorrhizal fungal partners in natural systems.
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Affiliation(s)
- Holly V. Moeller
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, CA, USA
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40
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Moeller HV, Peay KG. Competition-function tradeoffs in ectomycorrhizal fungi. PeerJ 2016; 4:e2270. [PMID: 27547573 DOI: 10.7717/peerj2270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023] Open
Abstract
Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining "high-quality" ectomycorrhizal fungal partners in natural systems.
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Affiliation(s)
- Holly V Moeller
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA; Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kabir G Peay
- Department of Biology, Stanford University , Stanford , CA , USA
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Revillini D, Gehring CA, Johnson NC. The role of locally adapted mycorrhizas and rhizobacteria in plant–soil feedback systems. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12668] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Revillini
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Catherine A. Gehring
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Nancy Collins Johnson
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
- School of Earth Sciences and Environmental Sustainability Northern Arizona University PO Box 5694 Flagstaff AZ 86011 USA
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Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol 2016; 7:238. [PMID: 26973616 PMCID: PMC4776211 DOI: 10.3389/fmicb.2016.00238] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/22/2022] Open
Abstract
The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.
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Affiliation(s)
- Annika C. Mosier
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Christopher S. Miller
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Kyle R. Frischkorn
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Robin A. Ohm
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Zhou Li
- Oak Ridge National LaboratoryOak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National LaboratoryKnoxville, TN, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Alla Lapidus
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Cindy Chen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Jenifer Johnson
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | | | - Chongle Pan
- Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Steven W. Singer
- Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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Henke C, Jung EM, Kothe E. Hartig' net formation of Tricholoma vaccinum-spruce ectomycorrhiza in hydroponic cultures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:19394-9. [PMID: 25791268 DOI: 10.1007/s11356-015-4354-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/09/2015] [Indexed: 05/27/2023]
Abstract
For re-forestation of metal-contaminated land, ectomycorrhizal trees may provide a solution. Hence, the study of the interaction is necessary to allow for comprehensive understanding of the mutually symbiotic features. On a structural level, hyphal mantle and the Hartig' net formed in the root apoplast are essential for plant protection and mycorrhizal functioning. As a model, we used the basidiomycete Tricholoma vaccinum and its host spruce (Picea abies). Using an optimized hydroponic cultivation system, both features could be visualized and lower stress response of the tree was obtained in non-challenged cultivation. Larger spaces in the apoplasts could be shown with high statistical significance. The easy accessibility will allow to address metal stress or molecular responses in both partners. Additionally, the proposed cultivation system will enable for other experimental applications like addressing flooding, biological interactions with helper bacteria, chemical signaling, or other biotic or abiotic challenges relevant in the natural habitat.
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Affiliation(s)
- Catarina Henke
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University, Neugasse 25, 07734, Jena, Germany.
| | - Elke-Martina Jung
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University, Neugasse 25, 07734, Jena, Germany
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University, Neugasse 25, 07734, Jena, Germany
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El Amrani A, Dumas AS, Wick LY, Yergeau E, Berthomé R. "Omics" Insights into PAH Degradation toward Improved Green Remediation Biotechnologies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11281-91. [PMID: 26352597 DOI: 10.1021/acs.est.5b01740] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review summarizes recent knowledge of polycyclic aromatic hydrocarbons (PAHs) biotransformation by microorganisms and plants. Whereas most research has focused on PAH degradation either by plants or microorganisms separately, this review specifically addresses the interactions of plants with their rhizosphere microbial communities. Indeed, plant roots release exudates that contain various nutritional and signaling molecules that influence bacterial and fungal populations. The complex interactions of these populations play a pivotal role in the biodegradation of high-molecular-weight PAHs and other complex molecules. Emerging integrative approaches, such as (meta-) genomics, (meta-) transcriptomics, (meta-) metabolomics, and (meta-) proteomics studies are discussed, emphasizing how "omics" approaches bring new insight into decipher molecular mechanisms of PAH degradation both at the single species and community levels. Such knowledge address new pictures on how organic molecules are cometabolically degraded in a complex ecosystem and should help in setting up novel decontamination strategies based on the rhizosphere interactions between plants and their microbial associates.
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Affiliation(s)
- Abdelhak El Amrani
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Anne-Sophie Dumas
- University of Rennes 1 , CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Lukas Y Wick
- UFZ, Department of Environmental Microbiology, Helmholtz Centre for Environmental Research , Permoserstraße 15, D-04318 Leipzig, Germany
| | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec Canada
| | - Richard Berthomé
- Plant Genomics Research Unit, UMR INRA 1165 - CNRS 8114 - UEVE , 2, Gaston Crémieux St., CP5708, 91057 Evry Cedex, France
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Plett JM, Martin F. Reconsidering mutualistic plant-fungal interactions through the lens of effector biology. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:45-50. [PMID: 26116975 DOI: 10.1016/j.pbi.2015.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/23/2015] [Accepted: 06/01/2015] [Indexed: 05/03/2023]
Abstract
Mutualistic mycorrhizal plant-fungal interactions have shaped the evolution of plant life on land. In these intimate associations, fungal hyphae grow invasively within plant tissues. Despite this invasion, these mycorrhizal fungi are not repulsed leading to a great deal of research focused on the signals exchanged between mutualistic fungi and their host plants in an effort to understand how these relationships are established. In this review, we focus on one type of signal used by mutualistic fungi during symbiosis: effector proteins. These small secreted proteins have recently been found to be used by a range of beneficial fungi to alter the physiological status of the plant host such that symbiosis is favoured. We discuss how the role of these novel proteins has altered our vision of how the 'mutualistic' lifestyle evolved in fungi: rather than being perceived as beneficial by their plant hosts, these microbes currently viewed as 'beneficial' may actually be overcoming the defences of their plant hosts in a mechanism originally thought to be unique to pathogenic microbes.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW 2753, Australia.
| | - Francis Martin
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280 Champenoux, France.
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Kuske CR, Hesse CN, Challacombe JF, Cullen D, Herr JR, Mueller RC, Tsang A, Vilgalys R. Prospects and challenges for fungal metatranscriptomics of complex communities. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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