A longitudinal roadside study of the New Hampshire alder root nodule microbiome

ABSTRACT Actinorhizal plants are pioneer plants that colonize harsh environments and have been used for land reclamation. Their ability to thrive under these harsh conditions is due to their symbiotic association with the nitrogen-fixing bacterium Frankia and forming a root nodule structure. Although the plant root nodule primarily contains the symbiont Frankia , other members of the nodule community have been identified. This study represents an investigation of the effects of different environments on the nodule microbiome of Alnus rugosa, a shrub actinorhizal tree found at different locations within New Hampshire over a 3-year period. We utilized 16S rRNA and ITS amplicon sequencing to map the seasonal bacterial and fungal communities in the A. rugosa root nodule microbiome compared to rhizosphere and bulk soil communities. The relative abundance of Frankiaceae in root nodules fluctuated seasonally and by site. Sites with lower relative abundance of Frankiaceae in nodules had higher relative abundances of fungal nodule occupants. The roadside bacterial communities were distinct from those at the rural site, with Chitinophagaceae and Nitrosomonadaceae being characteristic members of the roadside rhizospheres and bulk soils, respectively. Soil zinc significantly affected all microbial communities. Our results indicate that the A. rugosa root nodule and soil microbiomes are responsive to different environmental variables like roadways and other microorganisms, and these responses need to be further elucidated for the optimization of future in situ actinorhizal projects. IMPORTANCE Actinorhizal plants like alders are important ecologically and economically as pioneering plants. The symbiotic association with Frankia greatly accelerates the growth of the host plant and indirectly does the same for neighboring plants. Actinorhizal trees provide an excellent mechanism to restore disrupted environmental sites and have been used to reclaim land that has been used for strip-mines, gravel pits, and soil stabilization of other landscapes disturbed by the effects of erosion and water runoff. Actinorhizal plants are found on coastal lands around the estuaries, and some are proven to be salt tolerant. Elucidating the dynamics of microbial community structure of the alder root nodules will help our understanding of the ability of these pioneering plants to reclaim degraded lands and to survive in diverse harsh environments. The role that other members of actinorhizal plant root nodule plays may be important to that survival ability. This field study reports on the influence of soil variables, habitats, and seasons on the dynamics of the actinorhizal microbiome.