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Bacterial endophyte communities in the foliage of coast redwood and giant sequoia.

Carrell AA, Frank AC - Front Microbiol (2015)

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Life and Environmental Sciences, School of Natural Sciences, University of California, Merced Merced, CA, USA ; Department of Biology, Duke University Durham, NC, USA ; Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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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.

Mentions: We used principal coordinate analysis (PCoA) of weighted and unweighted UniFrac distances to investigate patterns of separation between endophyte communities in samples from the different locations (Figure 2). We found that unweighted UniFrac identified clustering by species (Figure 2B: Permanova: Pseudo-F statistic = 3.2009, P = 0.001; Anosim: R = 0.4557, P < 0.001). The CR communities formed two clusters that largely separated Northern and Central CA populations (Permanova: Pseudo-F statistic = 2.7375, P < 0.001; Anosim: R = 0.5349, P < 0.001), with some overlap. When we took into account the relative abundance of taxa in addition to the presence of bacterial taxa (using weighted UniFrac distance matrices) clustering by species still occurred (Figure 2B: Permanova: Pseudo-F statistic = 6.12, P = 0.001; Anosim: R = 0.5464, P < 0.001).


Bacterial endophyte communities in the foliage of coast redwood and giant sequoia.

Carrell AA, Frank AC - Front Microbiol (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585279&req=5

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.
Mentions: We used principal coordinate analysis (PCoA) of weighted and unweighted UniFrac distances to investigate patterns of separation between endophyte communities in samples from the different locations (Figure 2). We found that unweighted UniFrac identified clustering by species (Figure 2B: Permanova: Pseudo-F statistic = 3.2009, P = 0.001; Anosim: R = 0.4557, P < 0.001). The CR communities formed two clusters that largely separated Northern and Central CA populations (Permanova: Pseudo-F statistic = 2.7375, P < 0.001; Anosim: R = 0.5349, P < 0.001), with some overlap. When we took into account the relative abundance of taxa in addition to the presence of bacterial taxa (using weighted UniFrac distance matrices) clustering by species still occurred (Figure 2B: Permanova: Pseudo-F statistic = 6.12, P = 0.001; Anosim: R = 0.5464, P < 0.001).

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Life and Environmental Sciences, School of Natural Sciences, University of California, Merced Merced, CA, USA ; Department of Biology, Duke University Durham, NC, USA ; Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.

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.

No MeSH data available.


Related in: MedlinePlus