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PMID: 12542709 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater.

Environmental microbiology ·Vol. 5 ·No. 1 ·2003-01-00 ·Pages 13-24

Yan T, Fields MW, Wu L, Zu Y, Tiedje JM, Zhou J

Abstract

Nitrate-contaminated groundwater samples were analysed for nirK and nirS gene diversity. The samples differed with respect to nitrate, uranium, heavy metals, organic carbon content, pH and dissolved oxygen levels. A total of 958 nirK and 1162 nirS clones were screened by restriction fragment length polymorphism (RFLP) analysis: 48 and 143 distinct nirK and nirS clones, respectively, were obtained. A single dominant nirK restriction pattern was observed for all six samples and was 83% identical to the Hyphomicrobium zavarzinii nirK gene. A dominant nirS pattern was observed for four of the samples, including the background sample, and was 95% identical to the nirS of Alcaligenes faecalis. Diversity indices for nirK and nirS sequences were not related to any single geochemical characteristic, but results suggested that the diversity of nirK genes was inversely proportional to the diversity of nirS. Principal component analysis (PCA) of the sites based on geochemistry grouped the samples by low, moderate and high nitrate but PCA of the unique operational taxonomic units (OTUs) distributions grouped the samples differently. Many of the sequences were not closely related to previously observed genes and some phylogenetically related sequences were obtained from similar samples. The results indicated that the contaminated groundwater contained novel nirK and nirS sequences, functional diversity of both genes changed in relation to the contaminant gradient, but the nirK and nirS functional diversity was affected differently.

MeSH Terms

Bacteria/classification,enzymology,genetics Cloning, Molecular Fresh Water/chemistry,microbiology Genetic Variation Molecular Sequence Data Nitrates/metabolism Nitrite Reductases/genetics,metabolism Phylogeny Polymorphism, Restriction Fragment Length Sequence Analysis, DNA Uranium/metabolism Water Pollution, Chemical

Chemicals

Nitrates Uranium Nitrite Reductases nitrite reductase, copper-containing

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Yan Tingfen

Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS-6038, Bldg. 1505, TN 37831-6036, USA.

Fields Matthew W

Wu Liyou

Zu Yuangang

Tiedje James M

Zhou Jizhong

Article Info

Journal

Environmental microbiology

Abbr.

Environ Microbiol

ISSN

1462-2912

DOI

10.1046/j.1462-2920.2003.00393.x

Published

2003-01-00

Pages

13-24

Language

English

Region

England

NLM ID

100883692

Subset

Databases

GENBANK

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PubMed source DOI: 10.1046/j.1462-2920.2003.00393.x View journal details

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Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater.

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