title: Expression patterns of elemental cycling genes in the Amazon River Plume.
abstract: Metatranscriptomics and metagenomics data sets benchmarked with internal standards were used to characterize the expression patterns for biogeochemically relevant bacterial and archaeal genes mediating carbon, nitrogen, phosphorus and sulfur uptake and metabolism through the salinity gradient of the Amazon River Plume. The genes were identified in 48 metatranscriptomic and metagenomic data sets summing to >500 million quality-controlled reads from six locations in the plume ecosystem. The ratio of transcripts per gene copy (a direct measure of expression made possible by internal standard additions) showed that the free-living bacteria and archaea exhibited only small changes in the expression levels of biogeochemically relevant genes through the salinity and nutrient zones of the plume. In contrast, the expression levels of genes in particle-associated cells varied over orders of magnitude among the stations, with the largest differences measured for genes mediating aspects of nitrogen cycling (nifH, amtB and amoA) and phosphorus acquisition (pstC, phoX and phoU). Taxa varied in their baseline gene expression levels and extent of regulation, and most of the spatial variation in the expression level could be attributed to changes in gene regulation after removing the effect of shifting taxonomic composition. We hypothesize that changes in microbial element cycling along the Amazon River Plume are largely driven by shifting activities of particle-associated cells, with most activities peaking in the mesohaline regions where N2fixation rates are elevated.
authors.affiliation: Department of Microbiology, University of Georgia, Athens, GA, USA.
authors.forename: Brandon M
authors.initials: BM
authors.lastname: Satinsky
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Christa B
authors.initials: CB
authors.lastname: Smith
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Shalabh
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Marine
authors.initials: M
authors.lastname: Landa
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Patricia M
authors.initials: PM
authors.lastname: Medeiros
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.
authors.forename: Victoria J
authors.initials: VJ
authors.lastname: Coles
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Yager
authors.affiliation: College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA.
authors.forename: Byron C
authors.initials: BC
authors.lastname: Crump
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, GA, USA.
authors.forename: Mary Ann
authors.identifier: 0000-0002-0702-8167
authors.initials: MA
authors.lastname: Moran
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D017753:Ecosystem; D019848:Gene Expression Regulation, Archaeal; D015964:Gene Expression Regulation, Bacterial; D056186:Metagenomics; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation / Q000235:genetics; D010758:Phosphorus / Q000378:metabolism; D045483:Rivers / Q000382:microbiology*; D013455:Sulfur / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010758:Phosphorus; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen