Microbial Ecology in States of Health and Disease Workshop Summary (2014) / Chapter Skim
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A17 Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types--Neil R. Gottel, Hector F. Castro, Marilyn Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz, and Christopher W. Schadt
A17 Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types--Neil R. Gottel, Hector F. Castro, Marilyn Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz, and Christopher W. Schadt
Pages 412-434
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2011. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.
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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 fungal28S rRNA genes.
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. This study focuses on the root endophyte and the directly associated rhizosphere communities of two populations of Populus deltoides located in upland and bottomland sites near the Caney Fork River in central Tennessee.
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Materials and Methods Sites Description and Sample Collection Native P deltoides samples were collected in the basin of the Caney Fork River in the Buffalo Valley Recreation Area, downstream of the Center Hill Dam (bottomland site)
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Multiple root samples were collected from different lateral roots of each tree, with nine total samples at the upland site (labeled the U site) and 11 root samples at the bottomland site (labeled B site)
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For endophyte samples, 35 cycles were used instead of 30. Bacterial primers targeted the V4 region of the 16S rRNA gene, as described by Vishnivetskaya et al.
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Principal coordinate analysis (PCoA) was further performed using the Fast UniFrac metric and visualized by origin from either endophyte or rhizo sphere in both upland and bottomland sites by using the 3D Java KiNG image program (http://kinemage.biochem.duke.edu/software/)
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After initial processing, a total of 177,291 reads for bacterial endophytic samples and 100,311 reads for bacterial rhizosphere samples were generated in our pyrosequencing survey, with an average length read of 205 bp. In the fungal data set, after trimming and processing using mothur, 169,771 endophytic reads and 152,329 rhizosphere reads remained, with an average read length of 244 bp.
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No differences were apparent for arefaction curves r for microbial communities originating from upland versus bottomland sites. The fungal rarefaction curves displayed similar trends as the bacterial curves, with greater richness in the rhizosphere; however, endophytic samples were not as variable as the bacterial communities and on average contained more OTUs at equal sequencing depths (Figure A17-2)
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See Table S1 in the supplemental material for a more detailed breakdown of properties on a sample-by-sample basis.
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See Table S1 in the supplemental material for a more detailed breakdown of properties on a sample-by-sample basis.
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. Endophytic bacterial communities were heavily dominated by Proteobacteria at the phylum level, at >80% of the sequences in each sample, and Acidobacteria comprised only 6%.
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Fast UniFrac and OTU-Based Hierarchical Clustering Analyses Principal coordinate analysis generated by Fast UniFrac showed that the rhizosphere and endophyte bacterial and fungal communities form distinct clusters; within each of these clusters, the bottomland and upland communities exhibit considerable overlap (Figure A17-5)
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the phylogenetic classification and rarefaction results, where there were marked differences between the rhizosphere and endophytes but no consistent changes between the upland and bottomland sites. Correcting for multiple comparisons, UniFrac significance values for the bacterial data set significantly differed for the major treatments: endophyte versus rhizosphere and bottomland versus upland sites (see Table S2 in the supplemental material)
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Information on the identity of the major OTUs identified that are numbered and shown in Figure A17-6 can be also be found in Table S4 of the supplemental material. Discussion Very little is known about Populus interactions with the microbial community in mature, natural ecosystems, as most studies have originated from either FIGURE A17-6 Heat map and hierarchical cluster analysis based on the relative abundances of the top OTUs identified in >5 samples in the bacterial (A)
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Our results suggest that the diversity and composition of the associated microbial communities are largely consistent regardless of the differences in host trees and soil physicochemical characteristics associated with the two upland and bottomland sites studied and that the rhizosphere and endophyte communities are largely independent with little overlap in the dominant phyla or OTUs. These findings contradict previous reports that indicated soil properties are a major driver of differences in the distributions and compositions of microbial communities (Buyer et al., 2002; Jesus et al., 2010)
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deltoides in Contrasting Soils Rhizosphere bacterial samples were dominated by Acidobacteria and Proteo bacteria in both soil types, both of which are common phyla recovered from soil sequencing surveys (Castro et al., 2010; Janssen, 2006; Jesus et al., 2010) (Figure A17-3)
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. Our limited study of two contrasting soil types showed that both bacterial and fungal communities did not differ significantly in higher-order composition in either the rhizosphere or endosphere environment.
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, and the resulting community composition is affected by the surrounding soil and environmental properties. Therefore, if endophytes are mostly facultative rhizosphere organisms and/or accidental passengers within the root, then the rhizosphere and endosphere will have similar overall patterns of dominant phylogenetic groups and OTU abundance patterns.
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(2009) of plantationgrown Populus hybrids found differences in the rank abundance of different OTUs identified within roots and in bulk soils but also observed that over half of the ECM OTUs cooccurred in both habitats, even at the low sequencing depths achievable with clone library examinations.
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There appears to be little variation in dominant phyla within rhizosphere and endophyte habitats between the two soils and ecotypes of Populus examined thus far. Future work that includes more diverse soil types and the analysis of the specific effects of host genotype and chemical phenotypes should further elucidate the relative effects of environment and host factors in microbial associations with Populus.
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2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes.
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2007. Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils.
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