Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment

Environ Microbiol Rep. 2013 Oct;5(5):757-64. doi: 10.1111/1758-2229.12078. Epub 2013 Jul 22.

Abstract

In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing (SIP) approach. Methanotrophs in lake sediment were labelled using (13)CH4, and both labelled and unlabelled-RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled-RNA metatranscriptome was dominated by methanotroph sequences, particularly from Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.

MeSH terms

  • Aerobiosis
  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bacteria / metabolism
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Carbon Isotopes / analysis
  • Carbon Isotopes / metabolism
  • DNA, Bacterial / genetics
  • Geologic Sediments / microbiology*
  • Lakes / microbiology*
  • Metagenome
  • Methane / analysis
  • Methane / metabolism*
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Transcriptome*

Substances

  • Bacterial Proteins
  • Carbon Isotopes
  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • Methane