Temporal, spatial, and host-species variability in the conifer foliar endophyte community suggests airborne transmission of nitrogen-fixing symbionts
The foliar endophyte microbiomes of wild plants could play a key role in plant response to climate change, with particular importance for terrestrial carbon sinks such as high-latitude coniferous forests. Using 16S rRNA pyrosequencing, we previously found that the needles of Pinus flexilis growing at Niwot Ridge, CO were dominated by a few phylotypes of acetic acid bacteria (AAB), which may be responsible for demonstrated nitrogenase activity in P. flexilis twigs. Understanding host acquisition of AAB symbionts will be important to assess their ecological significance. The dominant AAB taxa are shared with the co-occurring conifer P. engelmanni, which could result from vertical endophyte transmission and co-divergence with pine hosts, or alternatively, from frequent horizontal transmission of broad host range endophytes (e.g. via air). To distinguish between these two alternatives, we used 16S rRNA Illumina sequencing to characterize the needle endophyte community at two additional time points (2102 and 2104), in one additional species (Pinus contorta) and at two additional sites (in the Eastern Sierras, CA). To improve the resolution of our 16S rRNA AAB sequences, we used a clustering-free approach that is appropriate for studying high-abundance community members in 16S Illumina data.
We detected five distinct AAB species in our data, with 93-97% identity to each other. All have less than 97% identity to known isolates. Within a year, the same AAB species dominated all samples, including those taken from different conifer species and at different geographic sites. In contrast, samples taken in different years were dominated by different AAB species. The sequences were identical to sequences sampled from air at Storm Peak Laboratories, CO, suggesting that the may be airborne. Our results are not consistent with pine-endophyte co-divergence; rather, they suggest that AAB endophyte communities are transmitted via air across large geographic distances.