Silicon Nanophotonics for Multi-Omic Marine Detection

The oceans are host to diverse marine microorganisms that are capable of cycling nearly all chemical elements and are responsible for over half of the oxygen on earth, forming a key part of our carbon cycle. Yet, studying the marine microbiome remains an outstanding challenge. Very few marine microbes have been successfully cultured under laboratory conditions and culture-independent methods like metagenomics and mass spectroscopy are incompatible with the real-time and in situ measurements necessary to study how physico-chemical drivers impact microbial nutrient cycling.<br/><br/>Here, we present our approach based on high quality factor silicon nanophotonics to simultaneously and rapidly measure multiple ‘omic’ signatures from marine ecosystems. Our metasurfaces are composed of sub-wavelength silicon nanobars on sapphire substrates. First, by introducing small biperiodic perturbations to the lateral block dimension, free space radiation can be coupled into guided mode resonances to produce high-Q resonances with Q factors exceeding 10³ in aquatic environments. We demonstrate in simulation and experiment that by varying the biperiodic perturbation from 10 nm to 50 nm, the quality factor can be modulated from 10²-10⁴ and that the local electric field can be driven to the silicon surface, increasing the overlap between the field and the binding surface by nearly four-fold. We experimentally demonstrate that by introducing tapered photonic mirrors, the resonator cavity length can be reduced by 10X while retaining Q-factors exceeding 3000, and that the long resonance lifetimes together with the increased field penetration at the binding surface results in strong spectral shifts of the resonance mode due to small perturbations to the local dielectric environment. We fabricate our metasurfaces by e-beam lithography and demonstrate that the optical responses of individual resonators can be spatially resolved as individually addressable finite ‘pixels’ and simultaneously read out on a 2D InGaAs CCD array in a cross-polarized reflection configuration.<br/><br/>Using this platform, we demonstrate quantitative and amplification-free detection of DNA and the harmful algae bloom toxin, microcystin, which poses a threat to drinking and agricultural water supplies. We selectively target nucleotides and the toxin microcystin on the same multiplexed platform using tailored surface functionalization of self-assembled monolayers (SAM) and a competitive antibody binding assay. We observe in both calculations and experiments that consecutive molecular layers generate 0.5 nm - 4 nm shifts to the resonant wavelengths as sequential layers bind to the resonator surface. Finally, I will discuss the integration of our high-Q metasurfaces with flow-through microfluidics and an autonomous robotic water sampler developed at the Monterey Bay Aquarium Research Institute (MBARI), that offers a pathway for in situ phycotoxin detection, processing, and analysis.