In root-nodule symbioses (RNS) between nitrogen (N) fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: 1) phylogenetic diversity of Frankia in soil vs. nodules, 2) change in Frankia assemblages in soil vs. nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and 3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages, and fell into two large clades not previously observed. Presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

Fungal species have numerous important functions in the environment. Where these functions occur will depend on how fungi are spatially distributed, but spatial structures of fungal communities are largely unknown. This is especially true in hyperdiverse tropical tree canopy systems, which are understudied using high-throughput sequencing technology. Here we explore fungal communities in a Costa Rican tropical rainforest canopy, with a focus on local-scale spatial structure and substrate specificity of fungi. We sampled 135 locations across five tree branches and identified fungi from four substrate types: outer host tree bark, inner bark, dead bryophyte tissue, and living bryophytes. Samples were located between one centimeter and eight meters apart. Fungal community composition and diversity varied among substrate types, even when multiple substrates were in direct contact. Fungi were most diverse in living bryophytes, with 39% of all fungal OTUs found exclusively in this substrate, and the least diverse in inner bark. Fungal communities had significant positive spatial autocorrelation and distance decay of similarity only at distances less than one meter. Similarity among samples declines by half in less than ten centimeters, and even at these short distances, similarities are low with few OTUs shared among samples. These results indicate that community turnover is high and occurs at very small spatial scales, with any two locations sharing very few fungi in common. High heterogeneity of fungal communities in space and among substrates may have important implications for the distributions, population dynamics, and diversity of other tree canopy organisms, including epiphytic plants.