Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA.
Department of Earth, Environmental, and Planetary Sciences, Rice University, Houston, Texas, USA.
mSystems. 2022 Aug 30;7(4):e0030122. doi: 10.1128/msystems.00301-22. Epub 2022 Jul 26.
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~10-fold by mineralogy and ~10-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.
土壤基质特性影响着养分循环、温室气体产生和土壤形成等微生物行为。然而，土壤的动态和异质性使得难以理清不同基质特性对微生物行为的影响。为了解决这一挑战，我们开发了一种可调节的人工土壤配方，并使用这些材料研究驱动土壤微生物生长和交流的非生物机制。当我们使用具有不同质地的标准化基质来培养气体报告生物传感器时，我们发现一种革兰氏阴性菌（大肠杆菌）在合成粉土中生长最好，在广泛的土壤基质势范围内保持活跃，而一种革兰氏阳性菌（枯草芽孢杆菌）更喜欢沙土，在低水势下孢子形成。土壤质地、矿物学和碱度都会减弱控制群落水平微生物行为的酰基高丝氨酸内酯（AHL）信号分子的生物可利用性。质地控制 AHL 感应的时间，而矿物学和碱度使 AHL 生物利用度降低了约 10 倍。最后，我们构建了一系列复杂程度不同的人工土壤，这些土壤的特性与一种黑钙土相似。随着人工土壤复杂性的增加，更接近黑钙土，微生物行为接近在自然土壤中发生的行为，只是有机物除外。理解土壤微生物的环境控制因素很困难，因为当比较不同的天然土壤时，许多非生物参数同时且不可控地变化，从而无法确定任何单个土壤参数对微生物行为的影响。我们描述了如何在人工土壤中单独改变土壤质地、矿物学、pH 值和有机物含量，以研究它们对土壤微生物的影响。使用报告稀有指示剂气体的微生物生物传感器，我们确定了控制微生物生长和减弱用于控制群落水平行为的可扩散化学物质生物利用度的土壤特性。我们发现人工土壤对革兰氏阴性（大肠杆菌）和革兰氏阳性（枯草芽孢杆菌）微生物的信号生物利用度和生长有不同的影响。这些人工土壤可用于研究控制土壤微生物适应性、信号传递和基因转移的机制。
