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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

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.
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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.

Mentions: Next, we examined our sequences for high-level taxonomic groups that consistently dominated our samples within or across locations. There were no significant differences in the distribution of the most common bacterial orders between locations or tree species (Figure 3). Acidobacteriales, Actinomycetales, Bacillales, Rhizobiales, Rhodospirillales, and Burkholderiales were the most abundant and diverse orders, each represented by over 100 OTUs, many of which could not be classified below the order level (e.g., 43% of the Actinomycetales OTUs, 35% of the Bacillales OTUs, 70% of the Rhizobiales OTUs).


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

Carrell AA, Frank AC - Front Microbiol (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

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

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.
Mentions: Next, we examined our sequences for high-level taxonomic groups that consistently dominated our samples within or across locations. There were no significant differences in the distribution of the most common bacterial orders between locations or tree species (Figure 3). Acidobacteriales, Actinomycetales, Bacillales, Rhizobiales, Rhodospirillales, and Burkholderiales were the most abundant and diverse orders, each represented by over 100 OTUs, many of which could not be classified below the order level (e.g., 43% of the Actinomycetales OTUs, 35% of the Bacillales OTUs, 70% of the Rhizobiales OTUs).

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