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Title: Isolating a functionally relevant guild of fungi from the root microbiome of Populus

Abstract

Plant roots interact with a bewilderingly complex community of microbes, including root-associated fungi that are essential for maintaining plant health. To improve understanding of the diversity of fungi in the rhizobiome of Populus deltoides, Populus trichocarpa and co-occurring plant hosts Quercus alba and Pinus taeda, we conducted field and greenhouse studies and sampled, isolated, and characterized the diversity of culturable root-associated fungi on these hosts. Using both general and selective isolation media we obtained more than 1800 fungal isolates from individual surface sterilized root tips. Sequences from the ITS and/or D1– D2 regions of the LSU rDNA were obtained from 1042 of the >1800 pure culture isolates and were compared to accessions in the NCBI nucleotide database and analyzed through phylogenetics for preliminary taxonomic identification. Sequences from these isolates were also compared to 454 sequence datasets obtained directly from the Populus rhizosphere and endosphere. Although most of the ectomycorrhizal taxa known to associate with Populus evaded isolation, many of the abundant sequence types from rhizosphere and endosphere 454 datasets were isolated, including novel species belonging to the Atractiellales. Isolation and identification of key endorrhizal fungi will enable more targeted study of plant-fungal interactions. Genome sequencing is currently underway for amore » subset of our culture library with the aim of understanding the mechanisms involved in host-endophyte establishment and function. As a result, this diverse culture library of fungal root associates will be a valuable resource for metagenomic research, experimentation and further studies on plant-fungal interactions.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [2]
  1. Michigan State Univ., East Lansing, MI (United States)
  2. Duke Univ., Durham, NC (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1327688
Alternate Identifier(s):
OSTI ID: 1328482
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Fungal Ecology
Additional Journal Information:
Journal Volume: 22; Journal Issue: C; Journal ID: ISSN 1754-5048
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Populus deltoides; Populus trichocarpa; endophytes; ectomycorrhizal fungi; ecological interactions; rhizobiome

Citation Formats

Bonito, Gregory, Hameed, Khalid, Ventura, Rafael, Krishnan, Jay, Schadt, Christopher W., and Vilgalys, Rytas. Isolating a functionally relevant guild of fungi from the root microbiome of Populus. United States: N. p., 2016. Web. doi:10.1016/j.funeco.2016.04.007.
Bonito, Gregory, Hameed, Khalid, Ventura, Rafael, Krishnan, Jay, Schadt, Christopher W., & Vilgalys, Rytas. Isolating a functionally relevant guild of fungi from the root microbiome of Populus. United States. doi:10.1016/j.funeco.2016.04.007.
Bonito, Gregory, Hameed, Khalid, Ventura, Rafael, Krishnan, Jay, Schadt, Christopher W., and Vilgalys, Rytas. Fri . "Isolating a functionally relevant guild of fungi from the root microbiome of Populus". United States. doi:10.1016/j.funeco.2016.04.007. https://www.osti.gov/servlets/purl/1327688.
@article{osti_1327688,
title = {Isolating a functionally relevant guild of fungi from the root microbiome of Populus},
author = {Bonito, Gregory and Hameed, Khalid and Ventura, Rafael and Krishnan, Jay and Schadt, Christopher W. and Vilgalys, Rytas},
abstractNote = {Plant roots interact with a bewilderingly complex community of microbes, including root-associated fungi that are essential for maintaining plant health. To improve understanding of the diversity of fungi in the rhizobiome of Populus deltoides, Populus trichocarpa and co-occurring plant hosts Quercus alba and Pinus taeda, we conducted field and greenhouse studies and sampled, isolated, and characterized the diversity of culturable root-associated fungi on these hosts. Using both general and selective isolation media we obtained more than 1800 fungal isolates from individual surface sterilized root tips. Sequences from the ITS and/or D1– D2 regions of the LSU rDNA were obtained from 1042 of the >1800 pure culture isolates and were compared to accessions in the NCBI nucleotide database and analyzed through phylogenetics for preliminary taxonomic identification. Sequences from these isolates were also compared to 454 sequence datasets obtained directly from the Populus rhizosphere and endosphere. Although most of the ectomycorrhizal taxa known to associate with Populus evaded isolation, many of the abundant sequence types from rhizosphere and endosphere 454 datasets were isolated, including novel species belonging to the Atractiellales. Isolation and identification of key endorrhizal fungi will enable more targeted study of plant-fungal interactions. Genome sequencing is currently underway for a subset of our culture library with the aim of understanding the mechanisms involved in host-endophyte establishment and function. As a result, this diverse culture library of fungal root associates will be a valuable resource for metagenomic research, experimentation and further studies on plant-fungal interactions.},
doi = {10.1016/j.funeco.2016.04.007},
journal = {Fungal Ecology},
number = C,
volume = 22,
place = {United States},
year = {2016},
month = {5}
}

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Works referencing / citing this record:

Phylogenetic and morphological analyses of the mycoparasitic genus  Piptocephalis
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Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities
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Phylogenetic and morphological analyses of the mycoparasitic genus  Piptocephalis
journal, January 2019


Differential growth promotion of poplar and birch inoculated with three dark septate endophytes in two trace element-contaminated soils
journal, May 2017

  • Berthelot, Charlotte; Blaudez, Damien; Leyval, Corinne
  • International Journal of Phytoremediation, Vol. 19, Issue 12
  • DOI: 10.1080/15226514.2017.1328392

Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities
journal, September 2018


Plant growth promotion, metabolite production and metal tolerance of dark septate endophytes isolated from metal-polluted poplar phytomanagement sites
journal, June 2016

  • Berthelot, Charlotte; Leyval, Corinne; Foulon, Julie
  • FEMS Microbiology Ecology, Vol. 92, Issue 10
  • DOI: 10.1093/femsec/fiw144