Roles of genotype-by-environment interactions in shaping the root-associated microbiome of Populus

Background/Question/Methods

Populus trees represents a genetically diverse, ecologically widespread riparian genus, that have potential as cellulosic feedstocks for biofuels, and contain the first tree species to have a full genome sequence. These trees are also host to a wide variety of symbiotic microbial associations within their roots and rhizosphere, thus may serve as ideal models to study the breadth and mechanisms of interactions between plants and microorganisms. However, most of our knowledge of Populus microbial associations to date comes from greenhouse and plantation-based trees; there have been no efforts to comprehensively describe microbial communities of mature natural populations of Populus. We have compared root endophyte and rhizosphere samples collected from two dozen sites within two watershed populations of Populus deltoides in Tennessee and North Carolina over multiple seasons. 454 pyrosequencing has been applied to survey and quantify the microbial community associated with P. deltoides, using primers targeting the bacterial 16S rRNA gene and the fungal 28S rRNA gene. Genetic relatedness among the Populus trees was evaluated using 20 SSR markers chosen for distribution across all 19 linkage groups of the Populus genetic map. Soil physical, chemical and nutrient status, as well as tree growth and age characteristics were also evaluated. 

Results/Conclusions

Root endosphere and rhizosphere communities have been found to be composed of distinct assemblages of bacteria and fungi with largely non-overlapping OTU distributions. Within these distinct endophyte and rhizosphere habitats, community structure is also influenced by soil characteristics, watershed origin and plant genotype; while observed seasonal influences have been minimal. We have isolated cultures of over a thousand bacteria and fungi from these environments representing most of the dominant community members insitu. Many of these isolates show distinct growth-promoting phenotypes with Populus. These findings indicate that the characteristics of the Populus root/soil environment may represent a relatively strong selective force in shaping endophyte and rhizosphere microbial communities and their functions may have great importance upon the success of Populus sp.  Forthcoming work in collaboration with JGI will explore more in depth the genetic basis of these associations within a common garden populations of P. trichocarpa containing over >1000 resequenced variants.