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Title: Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

Abstract

Analysis of metatranscriptomic and metagenomic datasets from the lower reaches of the Amazon River between Obidos and the river mouth revealed microbial transcript and gene pools dominated by Actinobacteria, Thaumarchaeota, Bacteroidetes, Acidobacteria, Betaproteobacteria, and Planctomycetes. Three mainstem stations spanning a 625 km reach had similar gene expression patterns (transcripts gene copy-1) across a diverse suite of element cycling genes, but two tributary-influenced stations at the mouth of the Tapajos River and near the Tocantins River at Belem had distinct transcriptome composition and expression ratios, particularly for genes encoding light-related energy capture (higher) and iron acquisition and ammonia oxidation (lower). Environmental parameters that were useful predictors of gene expression ratios included concentrations of lignin phenols, suspended sediments, nitrate, phosphate, and particulate organic carbon and nitrogen. Similar to the gene expression data, these chemical properties reflected highly homogeneous mainstem stations punctuated by distinct tributary- influenced stations at Tapajos and Belem. Although heterotrophic processes were expected to dominate in the lower Amazon, transcripts from photosynthetic bacteria were abundant in tributary-influenced regions, and transcripts from Thaumarcheota taxa genetically capable of chemosynthetic ammonia oxidation accounted for up to 21% of the transcriptome at others. Based on regressions of transcript numbers against gene numbers, expression ratiosmore » of Thaumarchaeota populations were largely unchanged within the mainstem, suggesting a relatively minor role for gene regulation. These quantitative gene and transcript inventories detail a diverse array of energy acquisition strategies and metabolic capabilities for bacteria and archaea populations of the world’s largest river system.« less

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1390438
Report Number(s):
PNNL-SA-128662
Journal ID: ISSN 2296-7745
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Frontiers in Marine Science; Journal Volume: 4
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Amazon; aquatic; bacteria; archaea; metabolism; energy acquisition; biology; carbon cycling; continuum; ecosystem; estuarine; genomic; gene expression; RNA; metagenome; metatranscriptome; coastal; interface; microbial; Photosynthesis; Respiration; terrestrial; tidal

Citation Formats

Satinsky, Brandon M., Smith, Christa B., Sharma, Shalabh, Ward, Nicholas D., Krusche, Alex V., Richey, Jeffrey E., Yager, Patricia L., Crump, Byron C., and Moran, Mary Ann. Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River. United States: N. p., 2017. Web. doi:10.3389/fmars.2017.00253.
Satinsky, Brandon M., Smith, Christa B., Sharma, Shalabh, Ward, Nicholas D., Krusche, Alex V., Richey, Jeffrey E., Yager, Patricia L., Crump, Byron C., & Moran, Mary Ann. Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River. United States. doi:10.3389/fmars.2017.00253.
Satinsky, Brandon M., Smith, Christa B., Sharma, Shalabh, Ward, Nicholas D., Krusche, Alex V., Richey, Jeffrey E., Yager, Patricia L., Crump, Byron C., and Moran, Mary Ann. Tue . "Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River". United States. doi:10.3389/fmars.2017.00253.
@article{osti_1390438,
title = {Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River},
author = {Satinsky, Brandon M. and Smith, Christa B. and Sharma, Shalabh and Ward, Nicholas D. and Krusche, Alex V. and Richey, Jeffrey E. and Yager, Patricia L. and Crump, Byron C. and Moran, Mary Ann},
abstractNote = {Analysis of metatranscriptomic and metagenomic datasets from the lower reaches of the Amazon River between Obidos and the river mouth revealed microbial transcript and gene pools dominated by Actinobacteria, Thaumarchaeota, Bacteroidetes, Acidobacteria, Betaproteobacteria, and Planctomycetes. Three mainstem stations spanning a 625 km reach had similar gene expression patterns (transcripts gene copy-1) across a diverse suite of element cycling genes, but two tributary-influenced stations at the mouth of the Tapajos River and near the Tocantins River at Belem had distinct transcriptome composition and expression ratios, particularly for genes encoding light-related energy capture (higher) and iron acquisition and ammonia oxidation (lower). Environmental parameters that were useful predictors of gene expression ratios included concentrations of lignin phenols, suspended sediments, nitrate, phosphate, and particulate organic carbon and nitrogen. Similar to the gene expression data, these chemical properties reflected highly homogeneous mainstem stations punctuated by distinct tributary- influenced stations at Tapajos and Belem. Although heterotrophic processes were expected to dominate in the lower Amazon, transcripts from photosynthetic bacteria were abundant in tributary-influenced regions, and transcripts from Thaumarcheota taxa genetically capable of chemosynthetic ammonia oxidation accounted for up to 21% of the transcriptome at others. Based on regressions of transcript numbers against gene numbers, expression ratios of Thaumarchaeota populations were largely unchanged within the mainstem, suggesting a relatively minor role for gene regulation. These quantitative gene and transcript inventories detail a diverse array of energy acquisition strategies and metabolic capabilities for bacteria and archaea populations of the world’s largest river system.},
doi = {10.3389/fmars.2017.00253},
journal = {Frontiers in Marine Science},
number = ,
volume = 4,
place = {United States},
year = {Tue Aug 08 00:00:00 EDT 2017},
month = {Tue Aug 08 00:00:00 EDT 2017}
}