Artificial soils reveal individual factor controls on microbial processes

Abstract

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 Gram-negative bacteria grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while Gram-positive bacteria preferred sandy soils, sporulating at a 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 ~105-fold by mineralogy and ~103-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. Properties that behaved additively were soil texture, pH, and mineralogy, while organic matter did not, suggesting that its soil behavior is an emergent property.

Non-destructive chemical sensing within bulk soil using 1000 biosensors per gram of matrix

“…Soils hydrated with minimal growth media, such as M63, exhibit water retention properties greatly exceeding those in natural soils because the osmotic pressure of minimal growth medium is higher than the aqueous phase of soils in situ . One way to overcome this challenge is to hydrate soils with diluted minimal medium, such as MIDV1 16 . To determine how hydration at a more realistic osmotic pressure affects the output from gas-reporting microbes, we evaluated the signal from soils hydrated to 64% field capacity using MIDV1 containing MG1655- mht (10 7 CFU/gram soil).…”

“…Studies analyzing CH 3 X production in liquid culture used a modified M63 medium 8 (pH = 7.0) containing 1 mM magnesium sulfate, 0.2% w/w glucose, 0.00005% w/w thiamine, 0.05% w/w casamino acids, 20% w/w M63 salt stock, and the indicated concentrations of NaCl or NaBr. Experiments in low-osmolarity medium used modified MIDV1 medium 16 (pH = 7.0), which contained 1 mM magnesium sulfate, 0.2% w/w glucose, 0.00005% w/w thiamine, 0.05% w/w casamino acids, 0.0125% w/w M63 salt stock, and the indicated concentrations of NaCl or NaBr. The M63 salt stock contained 75 mM ammonium sulfate, 0.5 M monobasic potassium phosphate, and 10 µM ferrous sulfate 12 .…”

“…To obtain a robust indicator gas signal from environmental matrices, prior gas reporter studies have all used twice-autoclaved matrices that are hydrated with a nutrientrich growth medium, which leads to osmolarities an order of magnitude above typical levels in the environment 8,12,16 . This growth medium has also been supplemented with halide salts at concentrations that are orders of magnitude higher than the levels found in natural matrices like soils 8,12,16,17 . Furthermore, biosensors have been added at titers that exceed the abundance of individual consortia members [18][19][20] and are on par with the total cell population in environmental matrices 1,21,22 .…”

“…Furthermore, biosensors have been added at titers that exceed the abundance of individual consortia members [18][19][20] and are on par with the total cell population in environmental matrices 1,21,22 . When environmental matrices are modified in these ways, the structure and function of the native microbiome is disrupted, limiting the utility of gas biosensors to monitor native microbial consortia without perturbation 16,[23][24][25] . To use biosensors under conditions that better reflect natural soil environments, there is a need to apply more sensitive detection methods to quantify trace indicator gas signals.…”

“…To date, MHT reporters have been used to study gene transfer in soil 8 , the effect of soil on the bioavailability of microbe-microbe signaling molecules 12 , and the effect of organic matter on the bioavailability of a microbe- plant signaling compound 15 . Additionally, MHTs have been used in synthetic soils to monitor the effects of different soil properties on the bioavailability of cell-cell signals 16 .…”