Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume

• Published in: PLOS ONE
• Main Authors: Zielinski, Brian L, Allen, Andrew E, Carpenter, Edward J, Coles, Victoria J, Crump, Byron C, Doherty, Mary, Foster, Rachel A, Goes, Joaquim I, Gomes, Helga R, Hood, Raleigh R, McCrow, John P, Montoya, Joseph P, Moustafa, Ahmed, Satinsky, Brandon M, Sharma, Shalabh, Smith, Christa B, Yager, Patricia L, Paul, John H
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Digital Commons @ University of South Florida 2016
• Subjects: Diatoms; Eukaryota; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Metagenome; Nitrogen; Nitrogen Fixation; Rivers; Transcriptome; Water Microbiology; Marine Biology; North Atlantic
• Online Access: https://digitalcommons.usf.edu/msc_facpub/236; https://doi.org/10.1371/journal.pone.0160929; https://digitalcommons.usf.edu/context/msc_facpub/article/1236/viewcontent/journal.pone.0160929.PDF

The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, ...