One of the main constraints is the difficulty in detecting and quantifying SMs in soil due to the matrix’s complexity in terms of microbial diversity, physical properties, and chemical composition. Despite extensive efforts to unravel how secondary metabolites impact microbiomes and soil processes, significant challenges persist in elucidating their precise roles in the natural environment. These metabolites allow microbes to engage in complex behaviors, such as cooperation, competition, and communication, which are important for shaping the composition and functionality of soil microbial communities. It is understood that in the spatially and temporally heterogenous environment of soil, microbes produce a plethora of specialized or secondary metabolites (SM) that can function as key mediators of microbial interactions. These communities encompass thousands of interacting species that mediate essential ecosystem services, ranging from biomass decomposition to crop productivity. Soil microbial communities play a pivotal role in biogeochemical cycles and ecosystem stability on a global scale. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. The transparent soil matrix allows the growth of B. subtilis chemical ecology under controllable soil-like conditions. Here, we describe a hydrogel-based transparent soil system to investigate B. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling.
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