Phenotypic and Genotypic Heterogeneity of Cyanobacterial Populations in Hot Spring Microbial Mats Revealed by Microfluidic Single-Cell Analysis

Abstract

The microbial mats found at Octopus Spring in Yellowstone National Park exhibit highly organized community structures. Thermophilic unicellular cyanobacteria (Synechococcus spp.), found in the 1-mm thick top layer of these hot spring mats, act as the primary producers in the microbial communities. The cyanobacterial population is an excellent model system for studying how environmental factors affect the structure of a microbial community because the system is relatively simple and formed under a well-defined set of environmental gradients such as temperature, oxygen and light levels. To obtain a detailed description of both phenotypic and genotypic structures of the population, we extended our microfluidic approach that has been previously developed for single-cell protein analysis of a similar type of cells [Huang et al., Science, 315, 81-84 (2007)]. First, a protein analysis chip was developed for simultaneous analysis of multiple single-cell lysates for higher throughput. We demonstrate that 16 cells can be analyzed individually during each round of analytical procedures to obtain phycobiliprotein distributions at the single-cell level. Second, a genetic analysis chip was designed to amplify genomic DNA from individual cyanobacteria cells via multiple displacement amplification. The presence of a selected set of genes was compared among populations under different environmental conditions. This type of single-cell genomic data is useful for elucidating the role of cyanobacterial species deduced from the metagenomic analysis of the microbial mat samples.