Bacteria inside semiconductors as potential sensor elements: biochip progress

Abstract

It was discovered at the beginning of this Century that living bacteria-and specifically the extremophile Pseudomonas syzgii-could be captured inside growing crystals of pure water-corroding semiconductors-specifically germanium-and thereby initiated pursuit of truly functional "biochip-based" biosensors. This observation was first made at the inside ultraviolet-illuminated walls of ultrapure water-flowing semiconductor fabrication facilities (fabs) and has since been, not as perfectly, replicated in simpler flow cell systems for chip manufacture, described here. Recognizing the potential importance of these adducts as optical switches, for example, or probes of metabolic events, the influences of the fabs and their components on the crystal nucleation and growth phenomena now identified are reviewed and discussed with regard to further research needs. For example, optical beams of current photonic circuits can be more easily modulated by integral embedded cells into electrical signals on semiconductors. Such research responds to a recently published Grand Challenge in ceramic science, designing and synthesizing oxide electronics, surfaces, interfaces and nanoscale structures that can be tuned by biological stimuli, to reveal phenomena not otherwise possible with conventional semiconductor electronics. This short review addresses only the fabrication facilities' features at the time of first production of these potential biochips.

Figure 1.

Germania-Pseudomonas syzgii compound crystals first observed forming in the University of Arizona fabrication facility in the year 2000.

Figure 2.

SEM images—From Left to Right: (a) Cultured Pseudomonas syzygii using R2A Media (Difco) growing in high quantity; No flow UltraPure Water (UPW) (b) Dried UPW on a Germanium (Ge) prism enclosed inside a Petri dish; (c) Single bacteria seen at various locations of the Ge surface (identical to bacteria in Arizona FAB).

Figure 3.

Flowchart representing nucleation, growth, and separation of bio-crystals.

Figure 4.

(As observed on the Ge prism)—From (1) Seeding due to the central bacterium in circular deposits (2) Growth of oxide-embedded seeds with bacteria (3) Crystal growth initiation after formation of square oxide moats (3b) Vast number of square oxide moats seen (4) Crystal formation in the center, shape depending upon the deposit morphology. (5) Formation of 3–5 micrometer bacterial crystals—Germanium Oxide crystals, with bacteria in majority of them (Inset).

Figure 5.

(Inclined SEM—at 75 Degrees): From left to right, showing an inclined SEM nucleation of the bacterial seeding at the center of the deposit, eventually forming bio-crystals.

Figure 6.

Exposures for more than 4 days showed corrosion crystals without bacterial entrapment.

Figure 7.

SEM images (A) pH = 5.5 at flow rate of 1 mL/min; Normal UPW pH = 7 (B) flow rate of 1 mL/min (C) flow rate of 2.5 mL/min and more.

Figure 8.

Following the same pattern as in Figure 7—MAIR-IR Spectra—A, B, C.

Figure 9.

XPS Spectrum showing the formation of a specific oxide of Ge—GeO₂ with Carbon and trace amounts of Si (from the flow cell)—(C1s at 284.6 eV for C-C, 286.4 eV for C-O, 288.6 eV for O=C-O; O1s peak at 531.9 eV for GeO₂; Ge3d at 32.7 eV for GeO₂; Si2p at 102.2 eV).