Abstract
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.
Methods
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.
Results
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.
Conclusions
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.
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Acknowledgements
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.
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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)
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Carper, D.L., Carrell, A.A., Kueppers, L.M. et al. Bacterial endophyte communities in Pinus flexilis are structured by host age, tissue type, and environmental factors. Plant Soil 428, 335–352 (2018). https://doi.org/10.1007/s11104-018-3682-x
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DOI: https://doi.org/10.1007/s11104-018-3682-x