Stable isotope probing to study functional components of complex microbial ecosystems

Sophie Mazard, Hendrik Schäfer

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

Abstract

This protocol presents a method of dissecting the DNA or RNA of key organisms involved in a specific biochemical process within a complex ecosystem. Stable isotope probing (SIP) allows the labelling and separation of nucleic acids from community members that are involved in important biochemical transformations, yet are often not the most numerically abundant members of a community. This pure culture-independent technique circumvents limitations of traditional microbial isolation techniques or data mining from large-scale whole-community metagenomic studies to tease out the identities and genomic repertoires of microorganisms participating in biological nutrient cycles. SIP experiments can be applied to virtually any ecosystem and biochemical pathway under investigation provided a suitable stable isotope substrate is available. This versatile methodology allows a wide range of analyses to be performed, from fatty-acid analyses, community structure and ecology studies, and targeted metagenomics involving nucleic acid sequencing. SIP experiments provide an effective alternative to large-scale whole-community metagenomic studies by specifically targeting the organisms or biochemical transformations of interest, thereby reducing the sequencing effort and time-consuming bioinformatics analyses of large datasets.

Original languageEnglish
Title of host publicationEnvironmental Microbiology
Subtitle of host publicationMethods and Protocols
EditorsIan T. Paulsen, Andrew J. Holmes
Place of PublicationTotowa, NJ
PublisherHumana Press
Pages169-180
Number of pages12
Edition2nd
ISBN (Electronic)9781627037129
ISBN (Print)9781627037112
DOIs
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1096
ISSN (Print)1064-3745

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