Browsing by Author "Cheng, Hsiao-Ying"

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    Biochar and Microbial Signaling: Production Conditions Determine Effects on Microbial Communication
    (American Chemical Society, 2013) Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.
    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell–cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.
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    Charcoal Disrupts Soil Microbial Communication through a Combination of Signal Sorption and Hydrolysis
    (American Chemical Society, 2016) Gao, Xiaodong; Cheng, Hsiao-Ying; Del Valle, Ilenne; Liu, Shirley; Masiello, Caroline A.; Silberg, Jonathan J.
    The presence of charcoal in soil triggers a range of biological effects that are not yet predictable, in part because it interferes with the functioning of chemical signals that microbes release into their environment to communicate. We do not fully understand the mechanisms by which charcoal alters the biologically available concentrations of these intercellular signals. Recently, charcoal has been shown to sorb the signaling molecules that microbes release, rendering them ineffective for intercellular communication. Here, we investigate a second, potentially more important mechanism of interference: signaling-molecule hydrolysis driven by charcoal-induced soil pH changes. We examined the effects of 10 charcoals on the bioavailable concentration of an acyl-homoserine lactone (AHL) used by many Gram-negative bacteria for cell–cell communication. We show that charcoals decrease the level of bioavailable AHL through sorption and pH-dependent hydrolysis of the lactone ring. We then built a quantitative model that predicts the half-lives of different microbial signaling compounds in the presence of charcoals varying in pH and surface area. Our model results suggest that the chemical effects of charcoal on pH-sensitive bacterial AHL signals will be fundamentally distinct from effects on pH-insensitive fungal signals, potentially leading to shifts in microbial community structures.
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    Using gas-producing enzymes to enable bacterial reporting within environmental matrices
    (2018-03-30) Cheng, Hsiao-Ying; Silberg, Jonathan J
    Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in biogeochemical cycles. Microbial behavior also affects soil development, water quality, and crop yields. The tools of synthetic biology have the potential to significantly improve our understanding of the roles that microbes play in these processes and the effects of environmental fluctuations on microbial behaviors, which can advance our ability to engineer microbial system for environmental applications, such as bioremediation, waste water treatment, and engineered rhizosphere. However, synthetic biology has not yet been widely used within environmental materials (soils, sediments, and biomass). One of the challenges is that there is a lack of robust and simple-to-detect reporter proteins for nontransparent and heterogeneous materials. Common genetic reporters used to read out circuit status have limited utility for in situ measurements in Earth materials because environmental matrices display high absorbance and auto-fluorescence at wavelengths of light used for visual reporters like GFP. This technical limitation has made it challenging to use programmed microbes to study how variation in soil environmental parameters (moisture, nutrient status, mineralogy, structure, and temperature) affect real-time biological behaviors. To overcome this limitation, my thesis research aims to develop a new reporting strategy using gas-producing enzymes, which generate diffusible gases that can be quantified in the headspace of soils using gas chromatography. First, I characterized the activities of two gas-producing enzyme, methyl halide transferase (MHT) and ethylene forming enzyme (EFE), in liquid media and an agricultural soil. Using these two enzymes, gas reporting strains were developed to monitor two dynamic soil microbial processes in situ, horizontal gene transfer and quorum sensing. These proof-of-concept applications demonstrate that the gas reporting method is a generalizable alternative to study microbial gene expression within soil where visual reporters are not compatible. I envision that this easy-to-use gas reporting method would facilitate the development of more sophisticated genetic circuits for applications in Earth, environmental, and planetary science