Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing

Methods Mol Biol. 2019:2046:163-174. doi: 10.1007/978-1-4939-9721-3_13.

Abstract

Metatranscriptomics is a powerful tool for capturing gene expression patterns in microbial communities and investigating their responses to environmental conditions. Stable isotope probing (SIP) is a method to target specific functional groups of microorganisms in environmental samples. The combination of RNA-SIP with metatranscriptomic analysis enhances the detection and identification of mRNA from target microorganisms. In this chapter we provide a protocol for RNA-SIP, mRNA enrichment, and mRNA preparation for high-throughput sequencing using an example of targeting methanotrophs in rice field soil.

Keywords: 13C-mRNA; High-throughput sequencing; Metatranscriptome; Soil microbiome; Stable isotope probing.

MeSH terms

  • Carbon Isotopes / metabolism
  • High-Throughput Nucleotide Sequencing
  • Isotope Labeling / methods*
  • Microbial Consortia / genetics
  • Microbial Consortia / physiology
  • Microbiota / genetics*
  • Microbiota / physiology
  • RNA, Bacterial / genetics
  • RNA, Bacterial / isolation & purification
  • RNA, Bacterial / metabolism
  • RNA-Seq / methods*
  • Soil Microbiology*
  • Transcriptome

Substances

  • Carbon Isotopes
  • RNA, Bacterial