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Title: Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype

Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems. We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing. Co-association patterns of fungal and bacterial taxa were assessed with 16S and ITS datasets. Community bipartite fungal-bacterial networks and PERMANOVA results attribute significant difference in fungal or bacterial communities to soil origin, soil chemical properties and plant genotype. Indicator species analysis identified a common set of root bacteria as well as endophytic and ectomycorrhizal fungi associated with Populus in different soils. However, no single taxon, or consortium of microbes, was indicative of a particular Populus genotype. Fungal-bacterial networks were over-represented in arbuscular mycorrhizal, endophytic, and ectomycorrhizal fungi, as well as bacteria belonging to the orders Rhizobiales, Chitinophagales, Cytophagales, and Burkholderiales. These results demonstrate the importancemore » of soil and plant genotype on fungal-bacterial networks in the belowground plant microbiome.« less
Authors:
 [1] ;  [1] ;  [2] ; ORCiD logo [3] ;  [3] ;  [4] ; ORCiD logo [3] ; ORCiD logo [5] ;  [2]
  1. Michigan State Univ., East Lansing, MI (United States); Great Lakes Bioenergy Research Center, East Lansing, MI (United States)
  2. Duke Univ., Durham, NC (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  4. Univ. of Florida, Quincy, FL (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 10; Journal Issue: 3; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Populus deltoides; fungal communities; bacterial communities; microbiome; NGS sequencing; arbuscular mycorrhizal fungi; endophytes; rhizosphere
OSTI Identifier:
1505327

Bonito, Gregory, Benucci, Gian Maria Niccolò, Hameed, Khalid, Weighill, Deborah A., Jones, Piet C., Chen, Ko -Hsuan, Jacobson, Daniel A., Schadt, Christopher Warren, and Vilgalys, Rytas. Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. United States: N. p., Web. doi:10.3389/fmicb.2019.00481.
Bonito, Gregory, Benucci, Gian Maria Niccolò, Hameed, Khalid, Weighill, Deborah A., Jones, Piet C., Chen, Ko -Hsuan, Jacobson, Daniel A., Schadt, Christopher Warren, & Vilgalys, Rytas. Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. United States. doi:10.3389/fmicb.2019.00481.
Bonito, Gregory, Benucci, Gian Maria Niccolò, Hameed, Khalid, Weighill, Deborah A., Jones, Piet C., Chen, Ko -Hsuan, Jacobson, Daniel A., Schadt, Christopher Warren, and Vilgalys, Rytas. 2019. "Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype". United States. doi:10.3389/fmicb.2019.00481. https://www.osti.gov/servlets/purl/1505327.
@article{osti_1505327,
title = {Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype},
author = {Bonito, Gregory and Benucci, Gian Maria Niccolò and Hameed, Khalid and Weighill, Deborah A. and Jones, Piet C. and Chen, Ko -Hsuan and Jacobson, Daniel A. and Schadt, Christopher Warren and Vilgalys, Rytas},
abstractNote = {Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems. We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing. Co-association patterns of fungal and bacterial taxa were assessed with 16S and ITS datasets. Community bipartite fungal-bacterial networks and PERMANOVA results attribute significant difference in fungal or bacterial communities to soil origin, soil chemical properties and plant genotype. Indicator species analysis identified a common set of root bacteria as well as endophytic and ectomycorrhizal fungi associated with Populus in different soils. However, no single taxon, or consortium of microbes, was indicative of a particular Populus genotype. Fungal-bacterial networks were over-represented in arbuscular mycorrhizal, endophytic, and ectomycorrhizal fungi, as well as bacteria belonging to the orders Rhizobiales, Chitinophagales, Cytophagales, and Burkholderiales. These results demonstrate the importance of soil and plant genotype on fungal-bacterial networks in the belowground plant microbiome.},
doi = {10.3389/fmicb.2019.00481},
journal = {Frontiers in Microbiology},
number = 3,
volume = 10,
place = {United States},
year = {2019},
month = {3}
}

Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010