Synthetic biology can pair with omics to understand mechanisms driving marine biogeochemical cycles

Caroline A Masiello, Rice University, Department of Earth, Environmental, and Planetary Sciences, Houston, TX, United States, Jonathan J Silberg, Rice University, BioSciences, Houston, TX, United States, Lauren Stadler, Rice University, Department of Civil and Environmental Engineering, Houston, TX, United States, David Shis, Rice University, Earth, Environmental and Planetary Sciences, Houston, TX, United States, Emily Marie Fulk, Rice University, Systems, Synthetic and Physical Biology, Houston, TX, United States, Ilenne Del Valle, Rice University, Systems, Synthetic, and Physical Biology, Houston, TX, United States, Xiaodong Gao, Rice University, Earth, Environmental, and Planetary Sciences, Houston, TX, United States and Li Chieh Lu, Rice University, Systems, Synthetic, and Physical Biology Program, Houston, United States
Abstract:
An explosion in synthetic biology tools is creating a broad range of new approaches to understand microbial behavior in the Earth system. These new tools can pair well with omics analyses, as omics provides a holistic, ecosystem-scale perspective and synthetic biology can be used to test specific, reductionist questions.

Synthetic biology tools can be used to program microbes to report on their environment, informing researchers when changes in gene expression have been triggered (e.g. in response to shifts in O2 or nutrients), or when microbes have participated in a specific step of an elemental cycle. Microbial biosensors can be programmed to detect a wide range of biogeochemical processes, including aspects of C cycling (biofilm production, methanogenesis, and synthesis of extracellular enzymes), N cycling (expression of enzymes within the N cycle) and reporting on cryptic aspects of S and Fe cycling. These tools can be used to test hypotheses generated by omics analyses, improving our understanding of microbes’ roles in elemental cycling. Synthetic biology tools also bring the potential for reporting on the environment from the perspective of a microbe, matching the measurement scale exactly to the scale that a microbe experiences. However, synthetic microbes have not yet seen wide use in marine science in part due to the nascent maturity of synthetic biological tools. Here we will describe the new types of tools available and discuss their potential uses in marine science. We will also describe the research needed in both marine science and synthetic biology to better connect useful tools with our community.

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