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. 2011 Sep;77(17):5934-44.
doi: 10.1128/AEM.05255-11. Epub 2011 Jul 15.

Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types

Neil R Gottel  1 , Hector F Castro, Marilyn Kerley, Zamin Yang, Dale A Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A Tuskan, Rytas Vilgalys, Mitchel J Doktycz, Christopher W Schadt
Affiliations

Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types

Neil R Gottel et al. Appl Environ Microbiol. 2011 Sep.

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, 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.

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Figures

Fig. 1.
Fig. 1.
Rarefaction curves for bacterial OTUs, clustering at 97% rRNA sequence similarity. Curves represent sequences for multiple samples of rhizospheric (A and B) or endophytic (C and D) communities originating from samples of either upland (A and C) or bottomland (B and D) trees. See Table S1 in the supplemental material for a more detailed breakdown of properties on a sample-by-sample basis.
Fig. 2.
Fig. 2.
Rarefaction curves for fungal OTUs, clustering at 95% rRNA sequence similarity. Curves represent sequences for multiple samples of rhizospheric (A and B) and endophytic (C and D) communities originating from samples of either upland (A and C) or bottomland (B and D) trees. See Table S1 in the supplemental material for a more detailed breakdown of properties on a sample-by-sample basis.
Fig. 3.
Fig. 3.
Bacterial classifications using the RDP classifier at 80% identity as implemented in mothur, shown at the phylum level except for Proteobacteria, which are classified by class. The charts represent average results for rhizospheric (A and B) and endophytic (C and D) or communities originating from samples of either bottomland (B and D) or upland (A and C) trees. To aid in distinguishing the colors, phylogenetic groups are presented in the same order in the pie charts (clockwise) as in the legend (top to bottom) in each subchart.
Fig. 4.
Fig. 4.
Fungal sequence classifications as identified from a consensus among the top BLAST scores against the SILVA LSU database. The charts represent average results for rhizospheric (A and B) or endophytic (C and D) or communities originating from samples of either bottomland (B and D) or upland (A and C) trees. To aid in distinguishing the colors, phylogenetic groups are presented in the same order in the pie charts (clockwise) as in the legend (top to bottom) in each subchart.
Fig. 5.
Fig. 5.
Principle coordinate analysis of bacterial (A) and fungal (B) communities, based on Fast UniFrac analysis. Circles are color coded by sample type: rhizosphere bottomland, green; rhizosphere upland, blue; endophyte bottomland, red; endophyte upland, yellow.
Fig. 6.
Fig. 6.
Heat map and hierarchical cluster analysis based on the relative abundances of the top OTUs identified in >5 samples in the bacterial (A) and fungal (B) data sets. Cluster analysis completely separated OTU abundance by endophyte or rhizosphere origin. OTUs highlighted in yellow are discussed in the text. For classification details of the OTUs depicted here, see Table S4 in the supplemental material.
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