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. 2015 Sep 22;6:1008.
doi: 10.3389/fmicb.2015.01008. eCollection 2015.

Bacterial Endophyte Communities in the Foliage of Coast Redwood and Giant Sequoia

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Free PMC article

Bacterial Endophyte Communities in the Foliage of Coast Redwood and Giant Sequoia

Alyssa A Carrell et al. Front Microbiol. .
Free PMC article

Abstract

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers in the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10-40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. The taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and tundra ecosystems.

Keywords: 16S rRNA; Sequoia sempervirens; Sequoiadendron giganteum; bacterial endophytes; foliage; giant sequoia; microbiome; redwood.

Figures

FIGURE 1
FIGURE 1
Bar chart showing the relative abundance of major phyla in all the samples as percentages of all 16S rRNA gene sequences recovered in our foliage samples. Each bar represents a sample, and letters A–I indicate individual trees (nine total), while L, M, and U indicate the canopy location from which the sample was taken (lower, middle, or upper).
FIGURE 2
FIGURE 2
Principal coordinate analysis (PCoA) of the (A) unweighted and (B) weighted UniFrac distance matrices. Points that are closer together on the ordination have communities that are more similar. Each point corresponds to a sample, and shapes correspond to host tree populations. Coast redwood (CR) samples are shown in pink, and giant sequoia (GS) samples are shown in gray.
FIGURE 3
FIGURE 3
Heatmap showing the 20 most dominant orders in our dataset and their average relative abundances as percentages of all 16S rRNA gene sequences recovered in our foliage samples, along with the total number of operational taxonomic units (OTUs) in each order. The number of OTUs in each order that could not be classified below the order level is shown within parenthesis. Color tones range from white to dark gray to indicate the highest to lowest relative abundance values.
FIGURE 4
FIGURE 4
Heatmap showing the 20 most dominant OTUs in our dataset, along with best matches in the GenBank 16S rRNA database, an indication if the top GenBank nr match was a sequence from the Hodkinson et al. (2012) or Nissinen et al. (2012) studies, and their status as core OTUs across all samples (ALL), GS samples, CR samples, Coast redwood from Northern CA (CRN) or Coast redwood from Central CA (CRC). Within parenthesis, the percentage of samples above which the OTU is present. Color tones range from warm (red) to cool (blue) to indicate the highest to lowest relative abundance values.
FIGURE 5
FIGURE 5
Individual OTU heatmaps for dominant and diverse classes, along with best matches in the GenBank 16S rRNA database and an indication when the top match to GenBank nr was to sequences from the Hodkinson et al. (2012) or Nissinen et al. (2012) studies. Here, colors represent the relative abundance of each OTU as a percentage of the total OTUs within each class. Color tones range from warm (red) to cool (blue) to indicate the highest to lowest relative abundance values. GS: Giant sequoia; CRN: Coast redwood from Northern CA; CRC: Coast redwood from Central CA. Five OTUs which were significantly more common in giant sequoia than in CR are marked with an asterisk.
FIGURE 6
FIGURE 6
Maximum likelihood tree inferred using the Alphaproteobacterial sequences in our dataset that occur above 50 times total. Nodes with bootstrap support at or above 80 are indicated with a gray circle. Taxa named ‘OTU’ and with terminal branches shown in solid lines are OTUs from our dataset. Other taxa are indicated by their GenBank accession number, and in the case of isolates of known species, by species name. Taxa from the Hodkinson et al. (2012) study of lichen-associated bacteria are marked ‘Hodkinson’ and appear in blue, and taxa from the Nissinen et al. (2012) study on endophytes of arctic plants are marked ‘Nissinen’ and appear in red. A red arrow indicates that the OTU is among the 20 most abundant in the dataset (Figure 4).

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