Jonathan (Joff) Silberg is the Stewart Memorial Professor at Rice University with appointments in the departments of Biosciences, Bioengineering, and Chemical & Biomolecular Engineering. His research group studies how to apply synthetic biology at the cell-material interface by programming electron transfer between cells and materials, programming cell-cell signaling using volatile chemicals, and programming consortia-scale information storage. Silberg serves as the director for the interdisciplinary Systems, Synthetic, and Physical Biology Ph.D. program, and directs two NSF-funded training programs, including a National Research Traineeship (NRT) in Bioelectronics (2018-present) and a Research Experience for Undergraduates (REU) in Bionetworks (2010-present). He is the recipient of an NSF CAREER Award (2012), the Rice University Presidential Mentoring Award (2014), and the Rice University Exemplary Faculty Award in Natural Sciences (2022).

Talk title: “Using Synthetic Biology to Program Microbes and Environmental Consortia For Real-Time Sensing and Actuation”

Abstract: The rapid diversification of synthetic biology tools holds promise in making some hard-to-solve environmental problems tractable. In this talk, I will discuss problems in the Earth and environmental sciences that could be addressed using engineered living microbes. Such synthetic cells have the potential to offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous materials (e.g., soil and sludge), monitoring pollutants in real time, tracking cryptic elemental cycling, and detecting dynamic cell-environment interactions. First, I will describe our efforts to overcome biological component limitations by creating new classes of electrical protein switches. Second, I will describe our efforts using these switches in synthetic electron transport chains to program microbes to convert environmental information into electrical information in real time within riverine samples. Finally, I will describe our efforts to develop a new class of catalytic RNA for programming consortia-scale information storage, such as data about participation in gene transfer, as well as our efforts to use catalytic RNA to control cell-cell signaling, information storage, and cell fitness. These synthetic biology approaches are expected to be broadly useful for programming microbial consortia for fast sensing and actuation within hard-to-image environmental and built materials.

 

Susannah Green Tringe is the Director of the Environmental Genomics and Systems Biology division at Lawrence Berkeley National Laboratory, as well as Director of the Center for Restoration of Soil Carbon by Precision Agricultural Strategies (RESTOR-C). She received her undergraduate degree in physics from Harvard University then went on to a Ph.D. in biophysics from Stanford University, and joined Berkeley Lab as a postdoc at the Joint Genome Institute in 2003. There, she developed techniques for using DNA sequence data for comparative analysis of whole microbial communities, rather than individual organisms. Tringe’s current research focuses on using nucleic acid sequence data to study communities of microbes from diverse environmental niches and understand their assembly and function, with the goal of harnessing them for improved environmental and agricultural outcomes. These studies involve a combination of field, lab, and computational approaches to link molecular data to ecosystem processes. Her major research interests include how microbes interact with plants to affect growth, health and stress resistance, how microbes influence greenhouse gas uptake and release in wetlands and agricultural systems, and how microbes can be exploited to enhance soil carbon storage and to break down natural and man-made contaminants.

Talk title: “Sequence-based Interrogation of Soil Microbiomes and Their Ecosystem Benefits”

Abstract: Plants roots and the soil they grow in are heavily colonized with microbes that play critical roles in nutrient cycling and transport as well as influencing plant growth and health. Molecular methods including DNA sequencing have begun to elucidate the forces governing the assembly and maintenance of plant and soil microbial communities, offering the opportunity for these microbial communities to be nurtured and manipulated to promote plant growth and health as well as soil health and ecosystem functions.

We have investigated the factors influencing greenhouse gas emissions from natural and managed wetland systems and find that gas fluxes represent a complex interplay of biological, chemical and physical factors that vary across habitats. Our results suggest considerable heterogeneity in fluxes even in physically proximate locations that have implications for the success of wetland preservation and restoration as a carbon storage strategy, particularly in the context of sea level rise.

In agricultural systems, we find that different plant compartments (e.g. rhizosphere and root endosphere) harbor unique and dynamic microbial communities heavily influenced by the soil, surrounding environment and host genotype. Abiotic stress, such as drought and low nitrogen, can alter both the composition of these communities and their interactions with each other and the plant. Our sequence-based characterizations of plant-associated communities have identified key populations that structure the community and respond dynamically to environmental changes, representing potential targets for improvement of plant resilience.

Current projects in the group aim to identify microbial interventions that will potentially decrease greenhouse gas emissions, increase soil carbon storage and improve crop yields.