Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Filters applied. Clear all
. 2014 Jul 4;5:333.
doi: 10.3389/fmicb.2014.00333. eCollection 2014.

Pinus Flexilis and Picea Engelmannii Share a Simple and Consistent Needle Endophyte Microbiota With a Potential Role in Nitrogen Fixation

Affiliations
Free PMC article

Pinus Flexilis and Picea Engelmannii Share a Simple and Consistent Needle Endophyte Microbiota With a Potential Role in Nitrogen Fixation

Alyssa A Carrell et al. Front Microbiol. .
Free PMC article

Abstract

Conifers predominantly occur on soils or in climates that are suboptimal for plant growth. This is generally attributed to symbioses with mycorrhizal fungi and to conifer adaptations, but recent experiments suggest that aboveground endophytic bacteria in conifers fix nitrogen (N) and affect host shoot tissue growth. Because most bacteria cannot be grown in the laboratory very little is known about conifer-endophyte associations in the wild. Pinus flexilis (limber pine) and Picea engelmannii (Engelmann spruce) growing in a subalpine, nutrient-limited environment are potential candidates for hosting endophytes with roles in N2 fixation and abiotic stress tolerance. We used 16S rRNA pyrosequencing to ask whether these conifers host a core of bacterial species that are consistently associated with conifer individuals and therefore potential mutualists. We found that while overall the endophyte communities clustered according to host species, both conifers were consistently dominated by the same phylotype, which made up 19-53% and 14-39% of the sequences in P. flexilis and P. engelmannii, respectively. This phylotype is related to Gluconacetobacter diazotrophicus and other N2 fixing acetic acid bacterial endophytes. The pattern observed for the P. flexilis and P. engelmannii needle microbiota-a small number of major species that are consistently associated with the host across individuals and species-is unprecedented for an endophyte community, and suggests a specialized beneficial endophyte function. One possibility is endophytic N fixation, which could help explain how conifers can grow in severely nitrogen-limited soil, and why some forest ecosystems accumulate more N than can be accounted for by known nitrogen input pathways.

Keywords: 16S rRNA; Acetobacteraceae; Picea; Pinus; bacterial endophytes; conifers; nitrogen; subalpine.

Figures

FIGURE 1
FIGURE 1
Rarefaction curves for WE and treeline samples. There is no apparent asymptote in the rarefaction curves, suggesting that the sequencing depth does not encompass the full extent of phylotype richness in each of the communities. However, the rarefaction curves suggest that the lower number of phylotypes recovered from treeline samples was not due to insufficient sampling. The high and low of the error bars represent one SD away from the mean.
FIGURE 2
FIGURE 2
Relative abundances of various major bacterial phyla and classes recovered from P. flexilis and P. engelmannii needles. Relative abundance of phyla (and classes of the Proteobacteria) was calculated as the percentage of sequences belonging to a particular lineage of all 16S rRNA gene sequences recovered from each sample.
FIGURE 3
FIGURE 3
Phylogeny of major Alphaproteobacterial sequences in our samples. Maximum likelihood phylogeny of Alphaproteobacterial sequences that occurred at least 100 times along with the three most closely related sequences from the GenBank 16S rRNA database (accession number indicated). Because our sequences are short (approximately 300 nt), many of our clades have low bootstrap support. Here, only bootstrap values above 50% are displayed. The tree is rooted with Burkholderia arboris.
FIGURE 4
FIGURE 4
Heatmap showing the 10 most dominant phylotypes and their average relative abundances as percentages of all sample 16S rRNA gene sequences recovered in our conifer needles samples. (A) P. flexilis, (B) P. engelmannii. Color tones range from cool (blue) to warm (red) to indicate the lowest to highest relative abundance values. Phylotypes were considered dominant if they were both highly abundant and occurred frequently in samples of a given conifer species. Abbreviations: PT = Phylotype, Acetobac = Acetobacteraceae, Acidobac = Acidobacteria/Acidobacteriaceae, Burkhold = Burkholderiaceae, Bacteriod = Bacteriodetes, Flexibacteraceae, Methylobac = Methylobacteriaceae, Cytophag = Cytophagacae, Sphingomonad = Sphingomonadaceae.
FIGURE 5
FIGURE 5
Shared and host species-specific phylotypes. Blue: phylotypes found in all P. engelmannii samples but not in any of the P. flexilis samples. Red: phylotypes found in all P. flexilis samples but not in any of the P. engelmannii samples. Purple: indicates phylotypes recovered from all samples (i.e., both species). An asterisk indicates that the phylotype is included in Figure 2.
FIGURE 6
FIGURE 6
PCoA and UniFrac analysis of the bacterial communities associated with conifer needles. (A–C) PCoA of the unweighted UniFrac distance matrix. Points that are closer together on the ordination have communities that are more similar. Each point corresponds to a sample, and shapes correspond to (A) host species, (B) elevation, and (C) location. (D) Hierarchical clustering of composite communities of the conifer species. Leaves are labeled by color according to host species: red, P. flexilis; blue, P. engelmannii.

Similar articles

See all similar articles

Cited by 19 articles

See all "Cited by" articles

References

    1. Anand R., Chanway C. P. (2013). N2-fixation and growth promotion in cedar colonized by an endophytic strain of Paenibacillus polymyxa. Biol. Fertil. Soils 49 235–239 10.1007/s00374-012-0735-9 - DOI
    1. Anand R., Grayston S., Chanway C. (2013). N2-fixation and seedling growth promotion of lodgepole pine by endophytic Paenibacillus polymyxa. Microb. Ecol. 66 369–374 10.1007/s00248-013-0196-1 - DOI - PubMed
    1. Ando S., Goto M., Meunchang S., Thongra-ar P., Fujiwara T., Hayashi H., et al. (2005). Detection of nifH squences in sugarcane (Saccharurnomcinarurn L.) and Pineapple (Ananas cornosus [L.] Merr.). Soil Sci. Plant Nutr. 51 303–308 10.1111/j.1747-0765.2005.tb00034.x - DOI
    1. Arnold A. E., Mejia L. C., Kyllo D., Rojas E. I., Maynard Z., Robbins N., et al. (2003). Fungal endophytes limit pathogen damage in a tropical tree. Proc. Natl. Acad. Sci. U.S.A. 100 15649-15654. 10.1073/pnas.2533483100 - DOI - PMC - PubMed
    1. Arshad M., Frankenberger W. T. (1991). Microbial production of plant hormones. Plant Soil 133 1–8 10.1007/BF00011893 - DOI

LinkOut - more resources

Feedback