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

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.

Evaluation of droplet digital PCR for characterizing plasmid reference material used for quantifying ammonia oxidizers and denitrifiers

“…N 2 O, with a global warming potential approximately 296 times higher than that of carbon dioxide, is an important greenhouse gas [8]. The nosZ gene, encoding the catalytic subunit of N 2 O reductase, and the nirS/K gene, encoding nitrite reductase, are widely used as functional markers for studying the abundance of bacteria able to metabolize N 2 O and NO, to better understand the main causes of N 2 O and NO emissions [9][10][11].…”

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths

“…The H 0 index considers the equitability of the OTU distribution, 1/D also considers both richness and abundance and Chao1 is a non-parametric estimation of OTU richness. However, composition and abundance may not be completely epitomized by clone distribution; therefore, measurements and indices were used for relative comparisons (Yan et al, 2003;Fields et al, 2006). Comparisons between clone libraries were made with different approaches.…”

“…Diversity and community function Microbial communities have been extensively characterized at uranium-contaminated sites (Abdelouas et al, 2000;Chang et al, 2001Chang et al, , 2005Elias et al, 2003;Nevin et al, 2003;Vrionis et al, 2005) including the OR-FRC (Yan et al, 2003;North et al, 2004;Fields et al, 2005Fields et al, , 2006Akob et al, 2007). In general, it is assumed that bacterial diversity will depend upon the degree of contamination and will change in structure and Partition of the total variation into six components: unexplained variation; 'pure' temporal variation; 'shared' variation between environment and time; 'pure' environmental variation; 'shared' variation between environment and space; and 'pure' spatial variation.…”

Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

“…The contaminants alter local bacterial populations by exerting selective pressure (Akob et al, 2007), but leave other populations intact (Bagwell et al, 2006). Many studies of this site have used culturing techniques (M. Fields et al, 2005;Spain et al 2007) and molecular biomarker analysis (Palumbo et al, 2004;Bagwell et al, 2006;Yan et al, 2003;Akob et al, 2007, Spain et al 2007 to examine the bacterial diversity and functional capabilities of bacteria present in the area, but none of these studies have been able to simultaneously examine the 4 diversity of multiple functional genes. The objective of this study is to examine the bacterial community structure in wells of varying contamination and to determine which contaminants have the greatest effects on bacterial diversity.…”