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Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing

  • Ang HuEmail author
  • Yahai Lu
  • Marcela Hernández García
  • Marc G. Dumont
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)

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.

Key words

Metatranscriptome Stable isotope probing Soil microbiome 13C-mRNA High-throughput sequencing 

References

  1. 1.
    Orsi WD, Edgcomb VP, Christman GD, Biddle JF (2013) Gene expression in the deep biosphere. Nature 499(7457):205–208CrossRefGoogle Scholar
  2. 2.
    Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J (2012) Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One 7(4):e36009CrossRefGoogle Scholar
  3. 3.
    Yu K, Zhang T (2012) Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS One 7(5):e38183CrossRefGoogle Scholar
  4. 4.
    Dumont MG, Pommerenke B, Casper P (2013) Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment. Environ Microbiol Rep 5(5):757–764PubMedGoogle Scholar
  5. 5.
    Fortunato CS, Huber JA (2016) Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME J 10(8):1925–1938CrossRefGoogle Scholar
  6. 6.
    Bradford LM, Vestergaard G, Táncsics A, Zhu B, Schloter M, Lueders T (2018) Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into microaerobic pollutant-degrading aquifer microbiota. Front Microbiol 9:2696CrossRefGoogle Scholar
  7. 7.
    Noll M, Matthies D, Frenzel P, Derakshani M, Liesack W (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7(3):382–395CrossRefGoogle Scholar
  8. 8.
    Ma K, Conrad R, Lu Y (2012) Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Appl Environ Microbiol 78(2):445–454CrossRefGoogle Scholar
  9. 9.
    Hernández M, Dumont MG, Yuan Q, Conrad R (2015) Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl Environ Microbiol 81(6):2244–2253CrossRefGoogle Scholar
  10. 10.
    Kolb S, Knief C, Stubner S, Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69(5):2423–2429CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ang Hu
    • 1
    Email author
  • Yahai Lu
    • 2
  • Marcela Hernández García
    • 3
    • 4
  • Marc G. Dumont
    • 4
  1. 1.College of Resources and EnvironmentHunan Agricultural UniversityChangshaChina
  2. 2.College of Urban and Environmental SciencesPeking UniversityBeijingChina
  3. 3.School of Biological SciencesUniversity of SouthamptonSouthamptonUK
  4. 4.Max-Planck-Institute for Terrestrial MicrobiologyMarburgGermany

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