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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

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.
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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.

Mentions: To identify dominant members of the endophyte communities and their distribution across samples, we looked for OTUs that were present in both high relative abundance and were consistently present (i.e., in >85% of samples) within a species or population (hereafter referred to as core OTUs). Figure 4 shows the overall 20 most common OTUs in our dataset, along with their status as core OTUs across all samples or within a population. In addition, to capture the dominance and variation of OTUs within major groups (Figure 4), but that were not necessarily among the 20 top OTUs in the entire dataset, we did this separately for the OTU-rich classes Acidobacteria, Actinobacteriia, Bacilli, Alphaproteobacteria, and Betaproteobacteria (Figure 4). The results are shown in Figure 5, where the relative abundance of each OTU is calculated as the percentages of total OTUs within each class. In both cases (Figures 4 and 5), the resulting OTU sequences were used to query the NCBI 16S rRNA and nr databases for matches to isolates or uncultured sequences described in peer-reviewed manuscripts.


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

Carrell AA, Frank AC - Front Microbiol (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4585279&req=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.
Mentions: To identify dominant members of the endophyte communities and their distribution across samples, we looked for OTUs that were present in both high relative abundance and were consistently present (i.e., in >85% of samples) within a species or population (hereafter referred to as core OTUs). Figure 4 shows the overall 20 most common OTUs in our dataset, along with their status as core OTUs across all samples or within a population. In addition, to capture the dominance and variation of OTUs within major groups (Figure 4), but that were not necessarily among the 20 top OTUs in the entire dataset, we did this separately for the OTU-rich classes Acidobacteria, Actinobacteriia, Bacilli, Alphaproteobacteria, and Betaproteobacteria (Figure 4). The results are shown in Figure 5, where the relative abundance of each OTU is calculated as the percentages of total OTUs within each class. In both cases (Figures 4 and 5), the resulting OTU sequences were used to query the NCBI 16S rRNA and nr databases for matches to isolates or uncultured sequences described in peer-reviewed manuscripts.

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