Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments

Smith, C. J., Nedwell, D. B., Dong, L. F. and Osborn, A. M. (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, 73 (11). pp. 3612-3622. ISSN 0099-2240

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Estuarine systems are the major conduits for the transfer of nitrate from agricultural and other terrestrial-anthropogenic sources into marine ecosystems. Within estuarine sediments some microbially driven processes (denitrification and anammox) result in the net removal of nitrogen from the environment, while others (dissimilatory nitrate reduction to ammonium) do not. In this study, molecular approaches have been used to investigate the diversity, abundance, and activity of the nitrate-reducing communities in sediments from the hypernutrified Colne estuary, United Kingdom, via analysis of nitrate and nitrite reductase genes and transcripts. Sequence analysis of cloned PCR-amplified narG, napA, and nrfA gene sequences showed the indigenous nitrate-reducing communities to be both phylogenetically diverse and also divergent from previously characterized nitrate reduction sequences in soils and offshore marine sediments and from cultured nitrate reducers. In both the narG and nrfA libraries, the majority of clones (48 and 50, respectively) were related to corresponding sequences from delta-proteobacteria. A suite of quantitative PCR primers and TaqMan probes was then developed to quantify phylotype-specific nitrate (narG and napA) and nitrite reductase (nirS and nrfA) gene and transcript numbers in sediments from three sites along the estuarine nitrate gradient. In general, both nitrate and nitrite reductase gene copy numbers were found to decline significantly (P < 0.05) from the estuary head towards the estuary mouth. The development and application, for the first time, of quantitative reverse transcription-PCR assays to quantify mRNA sequences in sediments revealed that transcript numbers for three of the five phylotypes quantified were greatest at the estuary head. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Keywords:Molecular structure, Nitrogen compounds, RNA, Sediments, Transcription, Estuarine sediments, Marine ecosystems, Nitrite reductase genes, Estuaries, messenger RNA, nitrate, nitrate reductase, nitrite, nitrite reductase, nitrogen, primer DNA, abundance, estuarine sediment, gene expression, phylogenetics, polymerase chain reaction, species diversity, agricultural species, article, Deltaproteobacteria, denitrification, estuarine species, gene library, gene sequence, genetic transcription, genetic variability, marine environment, molecular cloning, molecular dynamics, napA gene, narG gene, nirS gene, nonhuman, nrfa gene, nucleotide sequence, quantitative analysis, reduction, reverse transcription polymerase chain reaction, sediment, sequence analysis, Bacteria, Bacterial Proteins, Biodiversity, Cloning, Molecular, DNA, Bacterial, Geologic Sediments, Great Britain, Molecular Sequence Data, Nitrite Reductases, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, RNA, Bacterial, RNA, Messenger, Sequence Analysis, DNA, Water Microbiology, Colne Estuary, England, Essex England, Eurasia, Europe, United Kingdom, Western Europe, Deltaproteobacteria
Subjects:C Biological Sciences > C180 Ecology
C Biological Sciences > C500 Microbiology
Divisions:College of Science > School of Life Sciences
ID Code:8952
Deposited On:22 Apr 2013 09:49

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