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.
Highlights
The plant microbiome is essential to plant health (Turner et al, 2013; Berg, 2014; Peñuelas and Terradas, 2014), but the role of microbes colonizing most wild plants still remains unknown
Rarefaction plots did not saturate, indicating that we under-sampled the bacterial communities at the 97% operational taxonomic units (OTUs) level
While acetic acid bacteria (AAB) bacterial were only present at low relative abundance in coast redwood (CR) and giant sequoia (GS), we found that Lichen-Associated Rhizobiales-1 (LAR1), a potential N2 fixing lineage associated with lichen thalli (Hodkinson and Lutzoni, 2009), was both consistently associated with CR (Figure 5), and represented by diverse taxa (Figure 6)
Summary
The plant microbiome is essential to plant health (Turner et al, 2013; Berg, 2014; Peñuelas and Terradas, 2014), but the role of microbes colonizing most wild plants still remains unknown. While a number of studies have examined the fungal endophyte communities inside the leaves of forest trees (Ganley et al, 2004; Arnold et al, 2007; Oono et al, 2014; Qadri et al, 2014), Endophytes of redwood and giant sequoia less is known about the role and diversity of their bacterial counterparts. The motivation for studying endophytic microbiomes comes mainly from studies of agricultural crops: Over the last two decades or so, a number of studies—most of them focused on bacterial isolates—have demonstrated that endophytes can benefit plants and crop yield through enhanced nutrient uptake, disease suppression, increased abiotic stress tolerance, and direct stimulation of plant growth, all from within the plant tissues (Rosenblueth and Martinez-Romero, 2006; Hardoim et al, 2008; Reinhold-Hurek and Hurek, 2011). Many of the traits that influence this response can be microbially mediated, including defense, N-fixation, and abiotic stress tolerance (Friesen et al, 2011)
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