High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Xavier Mayali, Peter K. Weber, Eoin L. Brodie, Shalini Mabery, Paul D. Hoeprich, Jennifer Pett-Ridge

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

Most microorganisms remain uncultivated, and typically their ecological roles must be inferred from diversity and genomic studies. To directly measure functional roles of uncultivated microbes, we developed Chip-stable isotope probing (SIP), a high-sensitivity, high-throughput SIP method performed on a phylogenetic microarray (chip). This approach consists of microbial community incubations with isotopically labeled substrates, hybridization of the extracted community rRNA to a microarray and measurement of isotope incorporation-and therefore substrate use-by secondary ion mass spectrometer imaging (NanoSIMS). Laboratory experiments demonstrated that Chip-SIP can detect isotopic enrichment of 0.5 atom % 13 C and 0.1 atom % 15 N, thus permitting experiments with short incubation times and low substrate concentrations. We applied Chip-SIP analysis to a natural estuarine community and quantified amino acid, nucleic acid or fatty acid incorporation by 81 distinct microbial taxa, thus demonstrating that resource partitioning occurs with relatively simple organic substrates. The Chip-SIP approach expands the repertoire of stable isotope-enabled methods available to microbial ecologists and provides a means to test genomics-generated hypotheses about biogeochemical function in any natural environment.

Original languageEnglish (US)
Pages (from-to)1210-1221
Number of pages12
JournalISME Journal
Volume6
Issue number6
DOIs
StatePublished - Jun 2012
Externally publishedYes

Fingerprint

isotopic analysis
Microarray Analysis
resource use
Isotopes
stable isotopes
RNA
stable isotope
substrate
genomics
incubation
microorganisms
functional role
niche partitioning
nucleic acid
spectrometers
ecologists
nucleic acids
microbial communities
Genomics
microbial resource

Keywords

  • biogeochemistry
  • marine
  • microarray
  • microbial function
  • NanoSIMS
  • stable isotope probing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Microbiology

Cite this

Mayali, X., Weber, P. K., Brodie, E. L., Mabery, S., Hoeprich, P. D., & Pett-Ridge, J. (2012). High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME Journal, 6(6), 1210-1221. https://doi.org/10.1038/ismej.2011.175

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. / Mayali, Xavier; Weber, Peter K.; Brodie, Eoin L.; Mabery, Shalini; Hoeprich, Paul D.; Pett-Ridge, Jennifer.

In: ISME Journal, Vol. 6, No. 6, 06.2012, p. 1210-1221.

Research output: Contribution to journalArticle

Mayali, X, Weber, PK, Brodie, EL, Mabery, S, Hoeprich, PD & Pett-Ridge, J 2012, 'High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use', ISME Journal, vol. 6, no. 6, pp. 1210-1221. https://doi.org/10.1038/ismej.2011.175
Mayali X, Weber PK, Brodie EL, Mabery S, Hoeprich PD, Pett-Ridge J. High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME Journal. 2012 Jun;6(6):1210-1221. https://doi.org/10.1038/ismej.2011.175
Mayali, Xavier ; Weber, Peter K. ; Brodie, Eoin L. ; Mabery, Shalini ; Hoeprich, Paul D. ; Pett-Ridge, Jennifer. / High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. In: ISME Journal. 2012 ; Vol. 6, No. 6. pp. 1210-1221.
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