Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

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 a. 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 particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.

A microarray for assessing transcription from pelagic marine microbial taxa

“…The downregulation of idiA in oligotrophic taxa such as Prochlorococcus AS9601 (eHLII) and Alphaproteobacteria SAR11 clade strain HIMB59 (Supplementary Figure S6) in Fe amendments was consistent with the repression of the gene in Fereplete cultures (Bagg and Neilands, 1987;Webb et al, 2001;Smith et al, 2010;Thompson et al, 2011). In contrast, idiA transcription by more eutrophic Synechococcus RCC307-like (sub-cluster 5.3A, MellaFlores et al, 2011) and Pelagibacter HTCC7211-like genotypes was higher in the Fe-amendment.…”

“…In addition to contaminated soils, acid mine drainage sites and Antarctic soils (Yergeau et al, 2007;Mason et al, 2010;Xie et al, 2011), the GeoChip has been applied to detect microbial DNA and RNA in the marine environment (Lu et al, 2012;Wawrik et al, 2012). Aside from the PhyloChip, which targets 16S rRNA genes (Brodie et al, 2006), existing microarrays target a specific genus (Rinta-Kanto et al, 2011), a particular process (Tiquia et al, 2004;Moisander et al, 2006Moisander et al, , 2007Ward et al, 2007;Bulow et al, 2008;Wu et al, 2008;Bouskill et al, 2011;Abell et al, 2012) or ecosystem (Rich et al, 2008;Smith et al, 2010;Rich et al, 2011). A comprehensive microarray that targets functional genes across diverse pelagic marine microbial communities has not yet been reported.…”

“…The most common strategy is to search public nucleotide (nt) sequence databases (such as National Center for Biotechnology Information (NCBI)) using key words (Rhee et al, 2004;He et al, 2007;Wu et al, 2008;He et al, 2010;Smith et al, 2010). The resulting data sets, however, typically do not resemble the natural diversity of target genes, a problem that is exacerbated in undersampled environments.…”

Comparative Analysis of 16S rRNA andamoAGenes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

“…For gene expression analysis, total DNA and RNA were extracted from the same homogenized sample in a 1:9 volume ratio, respectively. Total RNA was isolated using a modified phenol-chloroform method (67). RNA was treated with DNase (Promega, Southampton, United Kingdom) and purified with a Qiagen RNeasy minikit (Qiagen, Valencia, CA).…”

Linking Seasonal Reduction of Microbial Diversity to Increase in Winter Temperature of Waters of a Chilean Patagonia Fjord

“…The structure of microbial communities in the ocean displays vertical and horizontal patterns associated with variations in physicochemical and biological conditions (Giovannoni and Stingl, 2005;Zinger et al, 2011;Walsh et al, 2015) that can be modified by variations in environmental factors over a range of time scales (Fuhrman et al, 2006(Fuhrman et al, , 2015Smith et al, 2010;Giovannoni and Vergin, 2012;Ottesen et al, 2012). At seasonal scale, marine microorganisms display recurrent patterns of diversity driven by abiotic and biotic factors depending on specific environments (Fuhrman et al, 2006(Fuhrman et al, , 2015Bryant et al, 2016;Bunse and Pinhassi, 2017).…”