Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Quantum Diamond EcoFAB Microscope for In Situ NMR of Root Exudate Molecules


Zhao Hao1, Hunter Ocker1, Nishanth Anand1, Emanuel Druga2, Benjamin Gilbert1* ([email protected]), and Ashok Ajoy2


1Lawrence Berkeley National Laboratory (LBNL); and 2University of California–Berkeley



The scientific goal of this project is to understand the causal relationships between root exudation, rhizosphere processes such as microbial nutrient cycling, and plant health. To achieve this goal, this project will design and validate a prototype “quantum sensing microscope” that is integrated within Fabricated Ecosystems (EcoFABs) for the chemical imaging of rhizosphere processes (Sasse et al. 2019). Quantum control of electronic and nuclear spins in diamond will yield sensors that non-destructively measure nuclear magnetic resonance (NMR) spectra of 13C-labeled root exudates and natural abundance 31P species.


The team has designed, constructed, and optimized a confocal quantum sensing microscope for rhizosphere bioimaging at LBNL. This confocal microscope has a spatial resolution better than 200 nm and uses the nitrogen-vacancy (NV) centers in a single-crystal diamond as the quantum NMR sensors that are controlled and interrogated using optically detected magnetic resonance (ODMR) spectroscopy. Researchers have achieved a long NV coherence time of over 5 ms and have observed strong hyperfine couplings with naturally abundant 15N nuclei indicating the potential of enhanced sensitivity with hyperpolarization (Ajoy et al. 2018). Researchers have developed a software user interface with all the pulse sequence control protocols (Rabi oscillation, spin-echo, dynamical decoupling XY8-N, correlation spectroscopy, and NV-NMR coherently averaged synchronized readout) to perform a series of the ODMR measurements of exemplary metabolite samples (Bucher et al. 2019; Glenn et al. 2018). The team has experimentally demonstrated the coherent control of NV electron spins for detection of paramagnetic ions and NMR-active nuclei. These studies were performed in aqueous solutions with a less than picoliter volume at high throughput (in seconds) with a negligible total power input, allowing the planned non-invasive rhizosphere observations. These results will be presented at Goldschmidt Lyon 2023, an international geochemistry conference.


Ajoy, A., et al. 2018. “Orientation-Independent Room Temperature Optical 13C Hyperpolarization in Powdered Diamond,” Science Advances 4(5), eaar5492.

Bucher, D. B., et al. 2019. “Quantum Diamond Spectrometer for Nanoscale NMR and ESR Spectroscopy,” Nature Protocols 14, 2707­–47.

Glenn, D. R., et al. 2018. “High-Resolution Magnetic Resonance Spectroscopy Using a Solid-State Spin Sensor,” Nature 555(7696), 351–54.

Sasse, J., et al. 2019. “Multilab EcoFAB Study Shows Highly Reproducible Physiology and Depletion of Soil Metabolites by a Model Grass,” New Phytologist 222(2), 1149–60.

Funding Information

This research was supported by the DOE Office of Science, Biological and Environmental Research (BER) Program, grant no. DE-AC02-05CH11231, and in part by previous breakthroughs obtained through the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy Contract No. DE-AC02-05CH11231.