Changes in microbiome assembly of the pioneer Andean tree Alnus acuminata under land degradation

Land degradation in the Andes threatens ecosystems and biodiversity. The recovery of these areas often depends on pioneer species such as Alnus acuminata, which relies on symbiotic microorganisms for nutrient acquisition and stress tolerance. Understanding how degradation affects its microbiome is crucial for effective restoration. This study investigated how a land-use trajectory involving deforestation and abandonment impacts the diversity and structure of bacterial communities associated with Alnus acuminata. Next-generation sequencing of 16 S rRNA gene amplicons was used to compare bacterial communities in bulk soil, roots, and root nodules between a native forest and degraded forest in the Ecuadorian Andes. Land degradation significantly altered bulk soil bacterial diversity and community structure, with pH and carbon content identified as key environmental drivers. Degraded soils were dominated by Actinomycetota, whereas native forest soils harbored more diverse communities, including Acidobacteriota and Pseudomonadota. While bacterial diversity in root and nodule endophytes remained stable across both sites, their community structures differed significantly between native and degraded forests. This shift reveals that the endophytic compartments harbour distinct bacterial consortia in the degraded environment, suggesting a potential role for host-related factors in shaping the microbiome under environmental stress. In the degraded forest, the endophytic microbiome was characterized by an enrichment of stress-resilient, pathogen-defending, and plant growth-promoting genera such as Micromonospora, Rahnella, Rhodanobacter, Mycobacterium, and Deinococcus. These findings suggest that the stability and composition of the Alnus acuminata microbiome may be linked to its ability to establish in nutrient-poor, degraded environments, highlighting the importance of plant-microbe associations in ecosystem recovery and providing a basis for further mechanistic and ecological studies on restoration outcomes.