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Abstract Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions. 

The encroachment of woody shrubs into grasslands is a phenomenon that has been occurring in the Chihuahuan Desert since the 1800s. Research shows that extensive livestock grazing and increased drought levels have acted as the main drivers of the grassland-to-shrubland transition. Very few studies have considered the impacts of such vegetation changes on microbial communities. Microbes play important ecosystem roles in nutrient cycling and carbon sequestration but also have the potential to act as pathogens. As the role of microbes in ecosystems is so important, it is crucial to understand the potential impacts of shrub encroachment on microbes and vice versa. Additionally, dryland microbes in general are understudied and as drylands cover over 40% of Earth’s land, understanding these microbes is of great ecological importance. The goal of this study was to assess microbial communities in shrub encroached systems in the Chihuahuan Desert to improve understanding of the ecological impacts of encroachment and increase general knowledge of dryland microbes. To conduct this study, soil samples were collected from sites dominated by black grama grass (Bouteloua eriopoda), sites dominated by honey mesquite shrubs (Prosopis glandulosa), and transition sites with both black grama and mesquite. DNA from soil samples was sequenced for bacteria (16S) and fungi (ITS2). Soil sampling was conducted through five sampling periods across a 10-month range to assess any potential seasonal variation in the microbial communities. In addition to DNA sequencing, microbial biomass and other environmental variables were collected. Statistical analyses were conducted to assess potential differences in microbial communities between vegetation types and seasons. Analyses included assessments of alpha and beta diversity, co-occurrence networks, and differential abundance analyses. Results show that there are significant changes in the microbial communities across vegetation types and seasons. Unique fungal and bacterial communities were identified in association with the different vegetation types, demonstrating that differences in vegetation influence microbial communities. Additionally, findings show that microbial communities are strongly impacted by seasons, showing decreases in biomass and changes to community composition in warm summer months compared to cooler months. Additionally, results show higher proportions of fungal pathogens in grass sites compared to other sites. Overall, this study demonstrates that microbial communities are influenced by shrub encroachment. As dryland microbial communities are often understudied, these findings can provide valuable insight into the ecology of dryland microbes and shrub-encroached systems.