Development of a novel single-cell omics platform for the investigation of microbial population heterogeneity during stress adaptation

• Applicant: Dr. Christian Trötschel, since 10/2015
• Subject Area: Microbial Ecology and Applied Microbiology
• Term: from 2013 to 2016
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 242490587

Microbes’ dynamic changes over time are of great importance for their survival and functions. With the development of omics technologies, including genomics, transcriptomics and proteomics, these tools have become very effective methods to monitor the adaptation of a cell population to changing conditions, such as nutrient supply or stress exposure. Since microbes usually live in a community, it is also critical to investigate the microbial population heterogeneity on the single cell level during adaptation and evolution; such studies hold great promise to provide substantially new insight into fundamental physiological processes in microorganisms as well as to accelerate the development of superior strains for industrial biotechnology by using microevolution. However, due to technical challenges, single cell omics analyses are currently far from trivial. A critical prerequisite for population studies is the ability to detect and separate sub-populations in a proper manner. In the last years, the combination of single cell extraction technique and Raman profiling technique (in short, single-cell Raman profiling) has matured to a highly competitive and complementary technique at resolving the dynamics of cells at individual level and to uncover population heterogeneities in comparison to established approaches like FACS. While Raman profiles provide discriminatory information for individual cells, other techniques such as genomics and proteomics are required to link this information to the biological background. Therefore, it seems rational to combine Raman sorting with subsequent omics analysis for investigating microbial populations as proposed in this grant application. We want to develop a novel platform that would possess the following advantages: (1) the utilization of non-invasive labeling techniques with improved sensitivity for cell classification according to various parameters (e.g. physiological activity or fitness) with Raman profiling, (2) the combination of omics and Raman profiling /sorting for analyses of dynamic processes on the single cell level (3) the consideration of both cell population and single cells for biological interpretation. The research models chosen are Nannochloropsis and C. glutamicum, two microbes with strong potentially for industrial biotechnology utilization. Consequently, the proof of principle studies shall allow obtaining superior strains in respect to biofuel production and stress adaptation. In this joint effort, Chinese’ single-cell manipulation platform and sequence analyses experiences, are combined with German’s strength in metabolic labeling and proteomic analyses. Therefore, it is expected to be an ideal joint-project for Sino-German collaboration.

• DFG Programme: Research Grants
• International Connection: China
• Participating Person: Professor Dr. Kang Ning
• Ehemaliger Antragsteller: Privatdozent Dr. Ansgar Poetsch, until 10/2015