Molecular and nanoparticle based probes are used in biology to image or track physiological processes through some measurable property of the molecule, ideally in manner that is minimally perturbing to the biological system. Metal ions offer a useful set of measurable properties, among them are their mass and isotopic signatures. Additionally, most metals are not native to biology thus offering a unique signal above the complex background. Although metals offer great potential as probes, they often need to be chelated or encapsulated to be attached and targeted to specific proteins or cells. Alongside the developments to utilize metal ion probes, there must be advances in methods to measure them. Here we report advances in inorganic probes and mass spectrometry methods as they apply to biological systems of intact microbes and plants within microfluidic devices. Our results leverage single particle/cell inductively coupled mass spectrometry (ICP-MS) methods to characterize probes and labeled microbes and laser ablation ICP-MS for identification and mapping of microbial communities in microfluidic devices and plant root systems. We have established probe development and analytical workflows at plant microbe interfaces with the goal to identify and quantify microbial communities in the rhizosphere.