Soil DNA studies often present a misleading view of microbial communities by failing to distinguish between live and dead bacterial cells. There is a critical gap in research on how the composition of dead cells diverges from that of living ones and which ecological factors drive these differences. Understanding the live/dead distinction is essential for gaining insights into soil biological activity and nutrient reservoirs. In this study, we employed flow cytometry with fluorescent labeling, which allowed us to obtain single-cell measurements from large samples and effectively differentiate between live and dead bacteria, focusing on the impact of proximity to desert plants on soil microbial communities. We specifically investigated three desert plants—Zygophyllumdumosum, Hammadascoparia, and Atriplexhalimus—and compared their influence to that of soil crust and bare soil. Our findings reveal that Proteobacteria and Actinobacteria phyla are abundant in both live and dead fractions. The diversity of live bacterial communities is significantly higher in samples near H.scoparia and A.halimus compared to Z.dumosum and soil crust. Each plant species forms distinct nutrient islands, which markedly influence bacterial composition and the live-to-dead cell ratio. Importantly, living bacterial cells are less abundant in soil crust and bare ground compared to those beneath H.scoparia and A.halimus. The nutrient-poor conditions of bare soil favor communities of phyla known for their long-term ecological persistence. Conversely, Z.dumosum correlates with a higher proportion of dead cells, underscoring a paradox in its influence on microbial dynamics. In conclusion, the live/dead ratio alone does not provide a complete picture of ecological processes. Our results assert the necessity of looking beyond total bacterial communities to comprehensively understand the key contributors to soil ecology and function.
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