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Title: Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.

Abstract

The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis,more » regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1]
  1. ORNL
  2. Duke University
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1024268
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 77; Journal Issue: 17; Journal ID: ISSN 0099--2240
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; ABUNDANCE; BACTERIA; COMMUNITIES; FUNGI; GENES; GREENHOUSES; MICROORGANISMS; ORIGIN; SOILS; TENNESSEE; TREES; Bacterial Communities; Fungal Communities; Populus deltoides

Citation Formats

Gottel, Neil R, Castro Gonzalez, Hector F, Kerley, Marilyn K, Yang, Zamin, Pelletier, Dale A, Podar, Mircea, Karpinets, Tatiana V, Uberbacher, Edward C, Tuskan, Gerald A, Vilgalys, Rytas, Doktycz, Mitchel John, and Schadt, Christopher Warren. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.. United States: N. p., 2011. Web. doi:10.1128/AEM.05255-11.
Gottel, Neil R, Castro Gonzalez, Hector F, Kerley, Marilyn K, Yang, Zamin, Pelletier, Dale A, Podar, Mircea, Karpinets, Tatiana V, Uberbacher, Edward C, Tuskan, Gerald A, Vilgalys, Rytas, Doktycz, Mitchel John, & Schadt, Christopher Warren. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.. United States. doi:10.1128/AEM.05255-11.
Gottel, Neil R, Castro Gonzalez, Hector F, Kerley, Marilyn K, Yang, Zamin, Pelletier, Dale A, Podar, Mircea, Karpinets, Tatiana V, Uberbacher, Edward C, Tuskan, Gerald A, Vilgalys, Rytas, Doktycz, Mitchel John, and Schadt, Christopher Warren. Sat . "Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.". United States. doi:10.1128/AEM.05255-11.
@article{osti_1024268,
title = {Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.},
author = {Gottel, Neil R and Castro Gonzalez, Hector F and Kerley, Marilyn K and Yang, Zamin and Pelletier, Dale A and Podar, Mircea and Karpinets, Tatiana V and Uberbacher, Edward C and Tuskan, Gerald A and Vilgalys, Rytas and Doktycz, Mitchel John and Schadt, Christopher Warren},
abstractNote = {The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.},
doi = {10.1128/AEM.05255-11},
journal = {Applied and Environmental Microbiology},
issn = {0099--2240},
number = 17,
volume = 77,
place = {United States},
year = {2011},
month = {1}
}