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Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen KH, Jacobson D, Schadt C, Vilgalys R. Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. Front Microbiol 2019; 10:481. [PMID: 30984119 PMCID: PMC6450171 DOI: 10.3389/fmicb.2019.00481] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/25/2019] [Indexed: 02/03/2023] Open
Abstract
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.
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Affiliation(s)
- Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Great Lakes Bioenergy Research Center, East Lansing, MI, United States
| | - Gian Maria Niccolò Benucci
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Great Lakes Bioenergy Research Center, East Lansing, MI, United States
| | - Khalid Hameed
- Department of Biology, Duke University, Durham, NC, United States
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Piet Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ko-Hsuan Chen
- Department of Soil and Water Sciences, University of Florida, Quincy, FL, United States
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Christopher Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen KH, Jacobson D, Schadt C, Vilgalys R. Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. Front Microbiol 2019. [PMID: 30984119 DOI: 10.3389/fmicb.2019.00481/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
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.
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Affiliation(s)
- Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, East Lansing, MI, United States
| | - Gian Maria Niccolò Benucci
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, East Lansing, MI, United States
| | - Khalid Hameed
- Department of Biology, Duke University, Durham, NC, United States
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Piet Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ko-Hsuan Chen
- Department of Soil and Water Sciences, University of Florida, Quincy, FL, United States
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Christopher Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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