High Coverage Expression Profiling (HiCEP) of Microbial Community Genomes in the Ocean

Abstract

How microbes respond to variable environmental conditions? This is a fundamental question to understand regulating mechanisms of biogeochemical cycles in the ocean. High coverage expression profiling (HiCEP) is an RNA fingerprinting method able to analyze microbial metabolic responses to various environmental conditions. Although HiCEP has been applied to various types of single organisms and revealed their responses to targeted conditions, there have been no reports on the application of this method to gene expression profiling of microbial communities. The HiCEP method can provide a unique way of analysis in metatranscriptomics. In this chapter, we provide a guidance of the HiCEP method for applying it to the omics-study of natural ecosystems. We experimentally obtained HiCEP data of prokaryotic communities in coastal surface seawater to show the feasibility of this application, indicating its methodological advantages in the analysis of metatranscriptome. In addition to high accuracy and reproducibility, this method can evaluate gene expression using either peak patterns or compositions of sequence clusters without annotation information, which enables us to highlight previously undescribed but showing distinctive expression in particular environmental conditions. The HiCEP-sequencing method can be a powerful tool for meta-omics studies in various types of environmental settings.