Microbial gene expression patterns in the Amazon River and Plume

• Main Author: Satinsky, Brandon Meyer
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: uga 2014
• Subjects: Amazon River; Amazon Plume; Ocean; Metatranscriptomics; Gene Expression; Gene Regulation; Microbial communities; RNA; Bacteria; Metagenomics; Biogeochemistry; Internal Standards; Burd; North Atlantic
• Online Access: http://hdl.handle.net/10724/31505; http://purl.galileo.usg.edu/uga_etd/satinsky_brandon_m_201412_phd

The Amazon River is the world’s largest river system and spans nearly 6,500 km across South America prior to discharging freshwater and nutrients into the ocean via a low salinity plume that covers 20% of the Western Tropical North Atlantic Ocean. Prokaryotes (bacteria and archaea) carry out critical ecological roles in both the marine and freshwater environments of the Amazon system, and govern critical aspects of energy production and consumption. This dissertation details improvements and expansion of meta-omics methodologies that enable studies of the composition and activity of microbial community, including protocols for the synthesis and use of internal standards. Using the improved metatranscriptomic and metagenomics method, three subsequent studies shed light on the roles of prokaryotes in the Amazon River and Plume. In one study, quantitative metatranscriptomics and metagenomics were used to generate the first fully quantitative inventories of microbial genes and transcripts in a natural ecosystem, detailing the patchiness found in the abundance and regulation of prokaryotic genes within a single water mass on the outer continental shelf. In another study, quantitative metatranscriptomics and metagenomics datasets generated from microbial communities in both free-living and particle-associated microenvironments at six Amazon Plume stations were used to detail transcriptional patterns of prokaryotic genes, finding that changes in both gene regulation within a taxon and shifts in taxonomy among stations drive the variability in expression. Further, microbial cells associated with particulate material experience more chemically dynamic conditions spatially in the Amazon plume than do free-living cells. The final study addresses patterns of gene expression for freshwater prokaryotic communities in the lower Amazon River. High expression ratios of genes related to nitrogen cycling by Thaumarchaea taxa suggest an important role for chemoautotrophic archaea in river biogeochemistry. PhD Microbiology Microbiology Mary Ann Moran Mary Ann Moran Eric Stabb Jan Mrazek Adrian Burd