Soil bacterial biodiversity characterization by flow cytometry: The bottleneck of cell extraction from soil

Abstract The importance of soil biodiversity is increasingly recognized in agriculture and natural resource research development. Yet, traditional assessments are costly time‐consuming, limiting the extent frequency sampling analysis space time. Flow cytometry (FCM) a powerful technique to characterize cell communities due its high robustness accuracy, requiring only short time for characterization. Therefore, FCM could expand capabilities by allowing characterization different aspects bacterial biodiversity. However, this implementation requires previous dispersion, separation purification bacteria from complex matrices. Moreover, monitoring programs or evaluation management practices require high‐throughput analysis. In context, processing protocols need consider not an adequate recovery undamaged, representative pure bacteria, but also short‐time requirements. Although have been reported over time, our knowledge, there no recommended extraction protocol FCM. We reviewed state‐of‐art use flow scientific used soil. analysed literature take stock diversity methodologies applications considering abundance, diversity, community structure functional properties. This review provides several lines evidence (SBB) characterization, highlighting potential studies on dynamics. highlights discusses most relevant constraints gaps that be considered SBB FCM, such as scale‐down, new reagents methods purification, threshold efficiency selection standardized validated protocol. proposed we provided detailed databases systematized information would useful community.