Plant and Soil

, Volume 428, Issue 1–2, pp 335–352 | Cite as

Bacterial endophyte communities in Pinus flexilis are structured by host age, tissue type, and environmental factors

  • Dana L. CarperEmail author
  • Alyssa A. Carrell
  • Lara M. Kueppers
  • A. Carolin Frank
Regular Article


Background and aims

Forest tree microbiomes are important to forest dynamics, diversity, and ecosystem processes. Mature limber pines (Pinus flexilis) host a core microbiome of acetic acid bacteria in their foliage, but the bacterial endophyte community structure, variation, and assembly across tree ontogeny is unknown. The aims of this study were to test if the core microbiome observed in adult P. flexilis is established at the seedling stage, if seedlings host different endophyte communities in root and shoot tissues, and how environmental factors structure seedling endophyte communities.


The 16S rRNA gene was sequenced to characterize the bacterial endophyte communities in roots and shoots of P. flexilis seedlings grown in plots at three elevations at Niwot Ridge, Colorado, subjected to experimental treatments (watering and heating). The data was compared to previously sequenced endophyte communities from adult tree foliage sampled in the same year and location.


Seedling shoots hosted a different core microbiome than adult tree foliage and were dominated by a few OTUs in the family Oxalobacteraceae, identical or closely related to strains with antifungal activity. Shoot and root communities significantly differed from each other but shared major OTUs. Watering but not warming restructured the seedling endophyte communities.


The results suggest differences in assembly and ecological function across conifer life stages. Seedlings may recruit endophytes to protect against fungi under increased soil moisture.


16S rRNA Endophytic bacteria Pinus flexilis Climate change Conifers 



This research was supported by National Science Foundation grant DEB-1442348 to ACF and LMK, and by an Office of Science (BER), US Department of Energy grant to LMK. We thank the Mountain Research Station and Niwot Ridge LTER at the University of Colorado, Boulder, for logistical support. Thanks to E. Brown, C. Castanha for field assistance. The sequencing was carried out by the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01.

Supplementary material

11104_2018_3682_Fig6_ESM.gif (25 kb)
Fig. S1

Rarefaction curve showing shoot- and root samples. There is no apparent asymptote in the rarefaction curve suggesting that the community was undersampled. Lower numbers of OTUs were recovered from shoots than roots. The error bars represent standard error. (GIF 25 kb)

11104_2018_3682_MOESM1_ESM.eps (33 kb)
High Resolution Image (EPS 33 kb)


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Dana L. Carper
    • 1
    Email author
  • Alyssa A. Carrell
    • 2
    • 3
    • 4
  • Lara M. Kueppers
    • 5
    • 6
  • A. Carolin Frank
    • 2
    • 5
  1. 1.Quantitative and Systems Biology ProgramUniversity of California MercedMercedUSA
  2. 2.Life and Environmental Sciences, School of Natural SciencesUniversity of California MercedMercedUSA
  3. 3.Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleUSA
  4. 4.Biosciences DivisionOak Ridge National LaboratoryOak RidgeUSA
  5. 5.Sierra Nevada Research InstituteUniversity of California MercedMercedUSA
  6. 6.Energy and Resources GroupUniversity of California, BerkeleyBerkeleyUSA

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