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Title: Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution

The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful formsmore » of nitrogen.« less
Authors:
 [1] ;  [1] ;  [1] ;  [2] ;  [3] ; ORCiD logo [1]
  1. Centro para el Estudio de Sistemas Marinos, Puerto Madryn (Argentina)
  2. Centro para el Estudio de Sistemas Marinos, Puerto Madryn (Argentina); CCT CONICET CENPAT, Puerto Madryn (Argentina)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Report Number(s):
PNNL-SA-125133
Journal ID: ISSN 1932-6203
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 13; Journal Issue: 11; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1489274

Calderoli, Priscila A., Espínola, Fernando J., Dionisi, Hebe M., Gil, Mónica N., Jansson, Janet K., and Lozada, Mariana. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. United States: N. p., Web. doi:10.1371/journal.pone.0207606.
Calderoli, Priscila A., Espínola, Fernando J., Dionisi, Hebe M., Gil, Mónica N., Jansson, Janet K., & Lozada, Mariana. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. United States. doi:10.1371/journal.pone.0207606.
Calderoli, Priscila A., Espínola, Fernando J., Dionisi, Hebe M., Gil, Mónica N., Jansson, Janet K., and Lozada, Mariana. 2018. "Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution". United States. doi:10.1371/journal.pone.0207606. https://www.osti.gov/servlets/purl/1489274.
@article{osti_1489274,
title = {Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution},
author = {Calderoli, Priscila A. and Espínola, Fernando J. and Dionisi, Hebe M. and Gil, Mónica N. and Jansson, Janet K. and Lozada, Mariana},
abstractNote = {The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.},
doi = {10.1371/journal.pone.0207606},
journal = {PLoS ONE},
number = 11,
volume = 13,
place = {United States},
year = {2018},
month = {11}
}

Works referenced in this record:

IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013
  • Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
  • Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
  • DOI: 10.1093/nar/gkt919

Clustal W and Clustal X version 2.0
journal, September 2007