X-ray spectroscopies are very powerful tools to determine the chemistry of complex dilute solutes in abiotic and biotic systems. We have assayed their suitability to monitor the chemistry of complex solutions in a live biotic system. The impact of the probe on cells was quantified for 4 different cellular organisms differing in their resistance level to environmental stresses. We show that none of the organisms tested can survive the radiation doses needed for the acquisition of meaningful spectroscopic data. Therefore, on one hand, X-ray spectroscopy cannot be applied to the monitoring of single cells, and cellular damages have to be taken into account in the interpretation of the evolution of such systems. On the other hand, due to the limited extension of X-ray induced cellular damages in the culture volume, it is possible to probe a population of live cells provided that the culture to beam probe ratio is large enough to minimize the impact of mortality on the evolution of the biological system. Our results suggest that it could be possible to probe the volume in the close vicinity of a cell without affecting its activity. Using this setup we could monitor the reduction of selenite by the X-ray sensitive bacterium, Agrobacterium tumefaciens strain C58, for 24 h. This method has a great potential to monitor the respiration of various metals, such as iron, manganese and arsenic, in situ under relevant environmental conditions by live microorganisms.