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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

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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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).

Mentions: To gain better taxonomic resolution for dominant Alphaproteobacterial OTUs (such as those belonging to LAR1 and AAB discussed above), we constructed a maximum likelihood phylogenetic tree from the Alphaproteobacterial sequences occurring more than 50 times in our samples, along with similar sequences in GenBank (≥96% identity). The phylogeny is shown in Figure 6. All Rhodospirillales sequences fell within the family Acetobacteraceae but could not be classified below the family level. Many were similar to sequences from Nissinen et al.’s (2012) study on arctic plants. Similarly, Rhizobiales sequences fell in uncultured lineages with the majority putatively in the LAR1 lineage commonly associated with lichens (Hodkinson et al., 2012). This includes some of the most common OTUs in our dataset (e.g., 1726 and 1284), which fell within clades together with LAR1 sequences. The sequences classified as belonging to the order Sphingomonadales also had matches to sequences from the study on arctic plants (Nissinen et al., 2012). While several of the Sphingomonadales OTUs were closely related (≥97% identity) to isolated bacteria (in the genus Sphingomonas), only one OTU in the Rhizobiales was closely related to known isolates (in the genus Methylobacterium). Similarly, only one OTU in the Rhodospirillales was closely related to an organism that has been cultured (in the genus Neoasaia).


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

Carrell AA, Frank AC - Front Microbiol (2015)

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).
© Copyright Policy
Related In: Results  -  Collection

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

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).
Mentions: To gain better taxonomic resolution for dominant Alphaproteobacterial OTUs (such as those belonging to LAR1 and AAB discussed above), we constructed a maximum likelihood phylogenetic tree from the Alphaproteobacterial sequences occurring more than 50 times in our samples, along with similar sequences in GenBank (≥96% identity). The phylogeny is shown in Figure 6. All Rhodospirillales sequences fell within the family Acetobacteraceae but could not be classified below the family level. Many were similar to sequences from Nissinen et al.’s (2012) study on arctic plants. Similarly, Rhizobiales sequences fell in uncultured lineages with the majority putatively in the LAR1 lineage commonly associated with lichens (Hodkinson et al., 2012). This includes some of the most common OTUs in our dataset (e.g., 1726 and 1284), which fell within clades together with LAR1 sequences. The sequences classified as belonging to the order Sphingomonadales also had matches to sequences from the study on arctic plants (Nissinen et al., 2012). While several of the Sphingomonadales OTUs were closely related (≥97% identity) to isolated bacteria (in the genus Sphingomonas), only one OTU in the Rhizobiales was closely related to known isolates (in the genus Methylobacterium). Similarly, only one OTU in the Rhodospirillales was closely related to an organism that has been cultured (in the genus Neoasaia).

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