A New Tool for Unraveling Mineral-Microbe Interactions: Atom Probe Tomography (APT)
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摘要: 矿物-微生物相互作用是地球系统中最为活跃的地质动力之一，对地球演化过程具有深远的影响，也是矿物学和地质微生物学领域最重要的交叉研究方向之一.要全面正确理解微生物与矿物之间的相互作用，重点之一在于揭示超微尺度下微生物如何影响矿物表面结构和物质组成的变化.尽管近年来矿物-微生物相互作用的研究取得了显著进展，但由于该相互作用涉及更小尺度的微观过程，在纳米甚至亚纳米尺度同时表征矿物结构、化学成分和微生物残存印记等方面仍面临巨大挑战，因此许多原理性和机制性问题依然亟待解决.近年来新兴的三维原子探针（APT）技术突破了这一分析极限，可在亚纳米（近原子）尺度实现对几乎所有元素/同位素同时成像与定量分析（检测限为10-6），可为重建矿物-微生物相互作用过程提供近原子尺度、高灵敏度分析.APT最初是在材料科学领域发展并得到广泛应用，近年来该技术在地球科学领域受到日益增多的关注.本文概述了APT的原理、发展和样品制备等基本内容，介绍了生物矿化的概念及相关研究，并重点讨论了APT技术在微生物矿化、地质微生物的残存信号识别、生物材料等矿物-微生物相互作用领域的重要应用.最后，客观总结了当前APT技术在矿物-微生物相互作用研究中的局限性和面临的问题，并展望这种超级原位微区分析技术在矿物-微生物研究领域的未来发展方向.Abstract: Mineral-microbe interaction (MMI) is one of the most dynamic geological processes driving the evolution of Earth's system, profoundly influencing Earth life's evolutionary processes. MMIs are also a key research focus in mineralogy and geomicrobiology. To fully understand the interactions between microbes and minerals, one of the critical areas is to decode how microorganisms affect the structural and compositional changes on mineral surfaces at an ultra-microscopic scale. Although significant progress has been made in the MMI studies in recent years, major challenges still remain due to the microscopic processes occurring at nanoscale and even sub-nanoscale levels. Simultaneous characterization of mineral structures, chemical compositions, and microbial remnants at these scales remains difficult, leaving many fundamental mechanistic questions unresolved. The emerging three-dimensional atom probe technology (APT) overcomes these limitations. APT enables near-atomic scale imaging and quantitative analysis of nearly all elements/isotopes simultaneously, with a detection limit as low as 10⁻⁶. This provides near-atomic scale, high-sensitivity analysis for research into mineral-microbe interactions. Originally developed and widely applied in materials science, APT has attracted increasing attention in the field of Earth sciences in recent years. This paper provides an overview of the principles, development, and sample preparation involved in APT, introduces the concept of biomineralization and related studies, and focuses on the key applications of APT technology in fields such as microbial mineralization, identifying geological microbial remnants, and biomaterials related to mineral-microbe interactions. Finally, we objectively summarize the current limitations and challenges of APT technology in the study of mineral-microbe interactions and explore the future development directions of this advanced in-situ micro-area technique in the field of mineral-microbe research.
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Key words:
- biomineralization /
- geomicrobiology /
- biominerals /
- biomaterials /
- cross-sphere research /
- nanoscience /
- mineralogy
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图 1 三维原子探针LEAP6000XR仪器全貌
设备来自中国地质大学（武汉）地质微生物与环境全国重点实验室
Fig. 1. Overview of the LEAP 6000XR three-dimensional atom probe instrument
图 2 矿物晶体的典型微观结构特征（左），以及常见成像分析技术的空间分辨率（右）
可见三维原子探针技术在现存所有微观技术手段中在分辨率与检测限方面都做到了极致.修改自Gault et al.（2021）
Fig. 2. Typical microstructural features of mineral crystals (left) and spatial resolution of common imaging analysis techniques (right)
图 3 生物矿化领域的结构实体层次和典型的空间表征技术
a. X射线计算机断层扫描（XCT）、同步辐射X射线计算机断层扫描（SXCT）、聚焦离子束‒扫描电子显微镜（FIB-SEM）、扫描透射电子显微镜（（S）TEM）、电子能量损失谱（EELS）、三维原子探针（APT）技术在样本大小和分辨率方面填补了矿化组织和生物界面3D成像的不同空白；b. 骨骼中不同层次的结构单元，从微观骨单元水平到小于单个胶原纤维的原子水平的不同特征，修改自Grandfield（2022）
Fig. 3. Hierarchical structural entities in biomineralization and typical spatial characterization techniques
图 4 APT技术在生物矿物研究中的应用实例
a. 石鳖牙齿中含有机纤维的代表性样品，显示C与Na或Mg的共存现象；b. 人体骨骼中Mg与胶原纤维之间存在紧密的空间联系；c. 人类牙釉质中Mg、Na、F和COH的纳米级元素分布图；d. 人类牙釉质微观结构中镁与有机物的分布特征及其界面性质：左图为镁‒无定形磷酸钙（Mg-ACP）晶间相中Na的等值面图；右图为C、Mg以及Mg-ACP晶间相中Mg的等值面图；e. 人体上颌骨中Ca、C和Na的元素分布图，表明在有机‒无机界面上，Na与骨骼的有机成分呈共存关系；f. 兔骨胶原纤维中C、N（代表胶原纤维）与Ca、P（代表矿物质）的原子级分布.矿物主要分布于胶原纤维的外部，同时在纤维内部可观察到矿物密度的周期性增加，Ca与P呈现约30 nm的周期性间距；g. 有孔虫方解石中有机‒矿物界面的元素分布特征；h. 方解石中的三维原子重建及元素等值面；i. 碳酸盐晶体中的晶体内几丁质等有机成分与水和水合氢分子形成离散簇的图像特征.参考文献见正文
Fig. 4. Applications of APT technology in biomineral research
图 5 APT技术在地质样品中有机质/微生物残存研究中的应用实例
a. 牙形石磷灰石尖端的C和N等浓度面分析结果，等值分别为N=2.0%（原子百分比）和C=0.7%（左图）；C和N在三个团簇中的浓度分布显示了其局部特征（右）；b. 细菌磁铁矿中FeO、C和N的三维分布图像，显示三者之间具有显著的依存关系，揭示了生物成因磁铁矿的独特化学特征.参考文献见正文
Fig. 5. Applications of APT technology in geological marker research
图 6 APT技术在生物材料研究中的应用实例
a. 象牙牙本质中大致平行于z轴方向的高密度有机纤维分布；b. 封存在金中的羟基磷灰石纳米颗粒，其中Au、Ag和0.6% Ca的等值面被标出（左），以及代表性yz平面上的垂直切片图像（右）；c. 在Au（黄色）基底上电沉积的磷酸钙涂层APT三维重建图（左）和沿z轴方向的一维原子浓度分布（右）；d. 退火前驱玻璃中ZrO的簇集现象（左），以及玻璃陶瓷中尖晶石（ZnAl₂O₄）晶体与ZrO₂相邻共存的结构特征（右）；e. 玻璃陶瓷中Zr、Si和Y的元素分布，清晰地显示钇元素在ZrO₂（红色箭头）和ZrO₂/SiO₂异相界面（绿色箭头）处的偏析现象；f. 含银纳米颗粒的金属基质纳米复合材料中，Al、V和Ag的元素分布特征.参考文献见正文
Fig. 6. Applications of APT Technology in Biomaterials Research
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