PCR Detection of Genes Encoding Nitrite Reductase in Denitrifying Bacteria

Hallin, Sara; Lindgren, Per-Eric

doi:10.1128/aem.65.4.1652-1657.1999

Cited by 396 publications

(136 citation statements)

References 35 publications

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“…The copper-type nitrite reductase has been found in various denitrifying bacteria, nitrifying bacteria [12], and archaea [30]. Most nirK genes have been described in three subdivisions (K, L, and Q) of the Proteobacteria [7,9,10,12]. For the most part, the phylogeny of NirK sequences in this study correlated with the phylogeny of 16S rRNA genes.…”

Section: Genetic Diversity Of Cu-type Nitrite Reductasesupporting

confidence: 66%

Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Song

Ward

2003

FEMS Microbiology Ecology

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Diversity of the functional genes encoding dissimilatory nitrite reductase was investigated for the first time in denitrifying halobenzoate degrading bacteria and in two 4-chlorobenzoate degrading denitrifying consortia. Nitrite reductase genes were PCR-amplified with degenerate primers (specific to the two different types of respiratory nitrite reductase, nirS and nirK), cloned and sequenced to determine which type of nitrite reductase was present in each isolate and consortium. Halobenzoate degrading isolates belonging to the genera Ochrobactrum, Ensifer and Mesorhizobium, as well as Pseudomonas mendocina CH91 were found to have nirK genes, which were closely related to the previously published nirK genes of Ochrobactrum anthropi, Achromobacter cycloclastes, Alcaligenes faecalis and Pseudomonas aureofaciens, respectively. The isolates assigned to the genera Acidovorax, Azoarcus and Thauera as well as all other species in the genera Thauera and Azoarcus contained nirS genes, which were closely related to the nirS genes from Pseudomonas stutzeri with some exceptions. In addition, only nirS genes were found in 4-chlorobenzoate degrading denitrifying consortia. Three different major terminal restriction fragments from the nirS genes were detected by terminal restriction fragment length polymorphism analysis of the consortia, and five different nirS genes were cloned from one consortium. Three nirS gene clones were closely related to nirS genes from Thauera chlorobenzoica, Azoarcus tolulyticus and Pseudomonas aeruginosa, respectively. The phylogeny of nir genes was not entirely congruent with the 16S rRNA phylogeny of the genera nor was it correlated with the ecological and geographical origins or isolation substrates used for isolation and enrichment of consortia.

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Section: Genetic Diversity Of Cu-type Nitrite Reductasesupporting

confidence: 66%

Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Song

Ward

2003

FEMS Microbiology Ecology

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“…Because denitrification is catalyzed by a diverse group of bacteria, archaea, and fungi (Zumft 1997), research on the abundance and diversity of denitrifiers in the environment has focused on the functional genes involved in the denitrification pathway. Although some studies have utilized the periplasmic and membranebound NO 3 À reductase genes (napA and narG) (Flanagan et al 1999, Gregory et al 2000, Mergel et al 2001) and a gene encoding nitrous oxide reductase (nosZ; Michotey et al 2000, Scala and Kerkhof 2000, Mergel et al 2001, Rich et al 2003, most molecular investigations of bacterial denitrification in natural environments (see review by Bothe et al 2000) have utilized nitrite reductase (nirS and nirK; Linne von Berg and Bothe 1992, Hallin and Lindgren 1999, Braker et al 2000, Michotey et al 2000, Mergel et al 2001, because it catalyses the first committed step that leads to a gaseous intermediate. The reduction of nitrite is catalyzed by either one of two entirely different enzymes in terms of structure and the prosthetic metal, the cytochrome cd1 (encoded by the gene nirS) and the copper-containing nitrite reductases (encoded by the gene nirK).…”

Section: Molecular Approachesmentioning

confidence: 99%

Methods for Measuring Denitrification: Diverse Approaches to a Difficult Problem

Groffman

Altabet

Böhlke

et al. 2006

Ecological Applications

819

754

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Denitrification, the reduction of the nitrogen (N) oxides, nitrate (NO3-) and nitrite (NO2-), to the gases nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2), is important to primary production, water quality, and the chemistry and physics of the atmosphere at ecosystem, landscape, regional, and global scales. Unfortunately, this process is very difficult to measure, and existing methods are problematic for different reasons in different places at different times. In this paper, we review the major approaches that have been taken to measure denitrification in terrestrial and aquatic environments and discuss the strengths, weaknesses, and future prospects for the different methods. Methodological approaches covered include (1) acetylene-based methods, (2) 15N tracers, (3) direct N2 quantification, (4) N2:Ar ratio quantification, (5) mass balance approaches, (6) stoichiometric approaches, (7) methods based on stable isotopes, (8) in situ gradients with atmospheric environmental tracers, and (9) molecular approaches. Our review makes it clear that the prospects for improved quantification of denitrification vary greatly in different environments and at different scales. While current methodology allows for the production of accurate estimates of denitrification at scales relevant to water and air quality and ecosystem fertility questions in some systems (e.g., aquatic sediments, well-defined aquifers), methodology for other systems, especially upland terrestrial areas, still needs development. Comparison of mass balance and stoichiometric approaches that constrain estimates of denitrification at large scales with point measurements (made using multiple methods), in multiple systems, is likely to propel more improvement in denitrification methods over the next few years.

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“…The multiple alignments of the nucleotide sequences for both copper and cytochrome cd-type nitrite reductase (nirK and nirS respectively) genes, including those recently deposited in public databases demonstrated that the previously constructed primers contained residues that were mismatched to recently identified sequences such as F1aCu, R3Cu (Hallin and Lindgren, 1999), 583F (Yan et al, 2003), nirK5R (Braker et al, 1998;Santoro et al, 2006) Heme 832F and Heme 1606R (Liu et al, 2003) for nirK genes, and Cd3aF (Michotey et al, 2000), F1aCu, R3Cd (Hallin and Lindgren, 1999;Throbäck et al, 2004), nirS1F, nirS6R (Braker et al, 1998), Copper 583F and Copper 909R (Liu et al, 2003) for nirS genes. However, it was difficult to design and establish novel primer sequences covering all of the nirK or nirS sequences present.…”

Section: Detection and Quantification Of Dissimilatory Nitrite Reductmentioning

confidence: 99%

Molecular biological and isotopic biogeochemical prognoses of the nitrification‐driven dynamic microbial nitrogen cycle in hadopelagic sediments

Nunoura

Nishizawa

Kikuchi

et al. 2013

Environmental Microbiology

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There has been much progress in understanding the nitrogen cycle in oceanic waters including the recent identification of ammonia-oxidizing archaea and anaerobic ammonia oxidizing (anammox) bacteria, and in the comprehensive estimation in abundance and activity of these microbial populations. However, compared with the nitrogen cycle in oceanic waters, there are fewer studies concerning the oceanic benthic nitrogen cycle. To further elucidate the dynamic nitrogen cycle in deep-sea sediments, a sediment core obtained from the Ogasawara Trench at a water depth of 9760 m was analysed in this study. The profiles obtained for the pore-water chemistry, and nitrogen and oxygen stable isotopic compositions of pore-water nitrate in the hadopelagic sediments could not be explained by the depth segregation of nitrifiers and nitrate reducers, suggesting the co-occurrence of nitrification and nitrate reduction in the shallowest nitrate reduction zone. The abundance of SSU rRNA and functional genes related to nitrification and denitrification are consistent with the co-occurrence of nitrification and nitrate reduction observed in the geochemical analyses. This study presents the first example of cooperation between aerobic and anaerobic nitrogen metabolism in the deep-sea sedimentary environments.

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PCR Detection of Genes Encoding Nitrite Reductase in Denitrifying Bacteria

Cited by 396 publications

References 35 publications

Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Methods for Measuring Denitrification: Diverse Approaches to a Difficult Problem

Molecular biological and isotopic biogeochemical prognoses of the nitrification‐driven dynamic microbial nitrogen cycle in hadopelagic sediments

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