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

• Published in: PloS one Vol. 13; no. 11; p. e0207606
• Main Authors: Calderoli, Priscila A, Espínola, Fernando J, Dionisi, Hebe M, Gil, Mónica N, Jansson, Janet K, Lozada, Mariana
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.11.2018; Public Library of Science (PLoS)
• Subjects: Alternation of generations; Anesthetic gases; Anesthetics; Archaea; Archaea - genetics; Archaea - isolation & purification; Archaeal Proteins - classification; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Argentina; Bacteria; Bacteria - genetics; Bacteria - isolation & purification; Bacterial Proteins - classification; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; BASIC BIOLOGICAL SCIENCES; Bays; Biology and Life Sciences; Biomarkers; Chemical properties; Climate change; Cluster Analysis; Coastal ecology; Coastal ecosystems; Coastal environments; Coastal sediments; Demographics; Denitrification; Denitrification - genetics; DNA - chemistry; DNA - isolation & purification; DNA - metabolism; Earth Sciences; Ecology; Ecology and Environmental Sciences; Ecosystems; Effluents; Environmental aspects; Enzymes; Gene sequencing; Genes; Genetic transformation; Genetic Variation; Genomics; Geologic Sediments - microbiology; Greenhouse gases; Hydrocarbons; Marine sediments; Metabolism; Metagenomics; Microbial activity; Microorganisms; Mitigation; Nitrate reduction; Nitrates; Nitrification; Nitrogen; Nitrogen (Chemical element); Nitrogen cycle; Nitrogen oxides; Nitrous oxide; Nitrous Oxide - metabolism; Nitrous oxides; Phylogeny; Physical Sciences; Pollution; Regulatory sequences; Research and Analysis Methods; Sediment pollution; Sediment samplers; Sediments; Sediments (Geology); Sequence Analysis, DNA; Transformation; Trends; Argentina; Tierra del Fuego
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0207606

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.