Microbial morphology fundamentally constrains how species interact with their environment, and hence ultimately affects their niche. However, the methodology of functional microbes in the soil ecosystem is still poorly studied since it is difficult to capture and identify the active monospecific community from the complicated environment and enormous number of microbial species in soils. To comprehensively reveal the morphology of active microbes in soil ecosystem, magnetic nanoparticle-mediated isolation (MMI) and single-cell image recognition (SCIR) were employed to study soil active Bacillus community, which functionally boosted the soil fertility in organic fertilisation compared to mineral fertilisation and unfertilised control treatments in our previous study. The results showed that MMI and SCIR can efficiently isolate active Bacillus from soil particles and other microorganisms. High throughput sequencing showed that the captured Bacillus showed similar community structure in different long-term fertilisation soils, while SCIR revealed that the active Bacillus was greater in number and larger in size in organic fertilisation treatment compared to mineral fertilisation and unfertilised control treatments. Our study demonstrates that the combination of MMI and SCIR is a potentially powerful tool to capture and identify the morphology of active and functional microbes in the soil ecosystem.

中文翻译：

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耦合磁性纳米粒子介导的分离和单细胞图像识别检测土壤中芽孢杆菌的细胞大小

微生物形态从根本上限制了物种与环境的相互作用，因此最终影响了它们的生态位。然而，由于难以从复杂的环境和土壤中大量的微生物物种中捕获和识别活跃的单特异性群落，土壤生态系统中功能微生物的方法学研究仍然很少。为全面揭示土壤生态系统中活性微生物的形态，采用磁性纳米粒子介导分离（MMI）和单细胞图像识别（SCIR）研究土壤活性芽孢杆菌社区，与我们之前研究中的矿物施肥和未施肥的对照处理相比，有机施肥在功能上提高了土壤肥力。结果表明，MMI和SCIR能有效地从土壤颗粒和其他微生物中分离出活性芽孢杆菌。高通量测序表明捕获的芽孢杆菌在不同的长期施肥土壤中表现出相似的群落结构，而SCIR显示活性芽孢杆菌与矿物施肥和未施肥的对照处理相比，有机施肥处理的数量和大小都更大。我们的研究表明，MMI 和 SCIR 的结合是一种潜在的强大工具，可以捕获和识别土壤生态系统中活性和功能微生物的形态。