Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by P inus sylvestris roots colonized by different ectomycorrhizal fungi

Summary Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of P inus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by R ussula sp. 6 GJ ‐2013b, P iloderma spp., M eliniomyces variabilis and P axillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were B urkholderia,   S phingopyxsis,   D yella,   P seudomonas,   A cinetobacter,   A ctinospica,   A quaspirillum,   A cidobacter   G p1 ,   S phingomonas,   T erriglobus,   E nhydrobacter,   H erbaspirillum and B radyrhizobium. Many genera had high initial abundance at week 8, declining with time but D yella and T erriglobus increased in abundance at later time points. In roots colonized by P iloderma spp. several other bacterial genera, such as A ctinospica , B radyrhizobium , A cidobacter   G p1 and R hizomicrobium appeared to increase in abundance at later sampling points.