Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin

Maria W. Smith, Lydie Herfort, Kaitlin Tyrol, Dominic Suciu, Victoria Campbell, Byron C. Crump, Tawnya Peterson, Peter Zuber, Antonio Baptista, Holly Simon

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll α. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particleattached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.

Original languageEnglish (US)
Article numbere13312
JournalPLoS One
Volume5
Issue number10
DOIs
StatePublished - 2010

Fingerprint

Archaeal Genes
Bacterial Genes
Columbia River
Salinity
Rivers
Gene expression
salinity
Gene Expression
Microbial Genes
gene expression
Transcriptome
Oceans and Seas
Estuaries
Microarrays
Oligonucleotide Array Sequence Analysis
Genes
oceans
Bacterial RNA
Water
Microbiota

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. / Smith, Maria W.; Herfort, Lydie; Tyrol, Kaitlin; Suciu, Dominic; Campbell, Victoria; Crump, Byron C.; Peterson, Tawnya; Zuber, Peter; Baptista, Antonio; Simon, Holly.

In: PLoS One, Vol. 5, No. 10, e13312, 2010.

Research output: Contribution to journalArticle

Smith, Maria W. ; Herfort, Lydie ; Tyrol, Kaitlin ; Suciu, Dominic ; Campbell, Victoria ; Crump, Byron C. ; Peterson, Tawnya ; Zuber, Peter ; Baptista, Antonio ; Simon, Holly. / Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. In: PLoS One. 2010 ; Vol. 5, No. 10.
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