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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

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).
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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).

Mentions: Across all samples, the most abundant phyla in all samples were Proteobacteria and Firmicutes, followed by Acidobacteria, Actinobacteria, TM7, and Bacteroidetes. The relative abundance of bacterial phyla varied among samples, but Proteobacteria or Firmicutes dominated most samples (Figure 1). Firmicutes were significantly more abundant in GS (35% of the sequences on average) than in CR (13% of the sequences on average; P < 0.05), and significantly different across locations (35, 22, and 6% of sequences from Freeman Creek, Central CA, and Northern CA, respectively; P < 0.005). Among the Proteobacteria, Alphaproteobacteria was the most prominent class, followed by Betaproteobacteria. Among the Firmicutes, Bacilli dominated.


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

Carrell AA, Frank AC - Front Microbiol (2015)

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).
© Copyright Policy
Related In: Results  -  Collection

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

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).
Mentions: Across all samples, the most abundant phyla in all samples were Proteobacteria and Firmicutes, followed by Acidobacteria, Actinobacteria, TM7, and Bacteroidetes. The relative abundance of bacterial phyla varied among samples, but Proteobacteria or Firmicutes dominated most samples (Figure 1). Firmicutes were significantly more abundant in GS (35% of the sequences on average) than in CR (13% of the sequences on average; P < 0.05), and significantly different across locations (35, 22, and 6% of sequences from Freeman Creek, Central CA, and Northern CA, respectively; P < 0.005). Among the Proteobacteria, Alphaproteobacteria was the most prominent class, followed by Betaproteobacteria. Among the Firmicutes, Bacilli dominated.

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