Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.

By I. N. Throbäck, Karin Enwall, Å. Jarvis, S. Hallin. FEMS Microbiology Ecology, 2004

1,335 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology, Pollution

View Paper: https://www.semanticscholar.org/paper/0499ea7069bfd7e1a15285629601cd3de92a5722

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Citations in the corpus

Identifying response groups of soil nitrifiers and denitrifiers to grazing and associated soil environmental drivers in Tibetan alpine meadows (2014, methodology): “, 1998) and cd3aF/R3cu (Throback et al., 2004) were used for the amplification of archaeal amoA gene, bacterial amoA gene, and nirK and nirS gene fragments, respectively.”
Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing (2014, neutral): “…30 sb; 40 cycles: 95 ◦C 15 s, 61 ◦C 30 s, 72 ◦C 30 s, 80 ◦C 30 sb; 1 cycle: 95 ◦C 15 s, 60 ◦C 30 s, 72 ◦C 10 min Melting curve: 60–95 ◦C nosZF nosZ1622R nosZ 453 Kloos et al. (2001), Throbäck et al. (2004) 1 cycle: 95 ◦C 10 min; 40 cycles: 95 ◦C 15 s; 61.5 ◦C 30 s; 72 ◦C 30 s Melting curve: 75–95…”
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil (2020, methodology): “The genes encoding 16S rRNA and the three 237 denitrification reductases nirK, nirS and nosZ clade I were quantified by qPCR using the 238 primers 27F and 518R for the 16S rRNA gene [63], 517F and 1055R for the nirK gene [64], 239 cd3aF and R3cd for the nirS gene [65] and Z-F and 1622R for the nosZ ”
Methods for measuring denitrification: diverse approaches to a difficult problem. (2006, methodology): “…analysis on a functional level with PCRamplified functional genes such as nirS and nosZ have been used with subsequent T-RFLP analysis (Scala and Kerkhof 2000, Braker et al. 2001, Rich et al. 2003, Wolsing and Prieme 2004) or by DGGE (Throback et al. 2004) to monitor community differences.”
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies (2006, methodology): “This has already led researchers to use functional genes, such as the [NiFe] hydrogenase gene, amoA, pmoA, nirS, nirK, nosZ, and pufM, in conjunction with DGGE (1, 19, 22, 39, 41) and to detect pmoA and dysB mRNAs with CARD-FISH (14, 26), leading the way for in situ identification of protein-encodin”
Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils (2012, background): “PCR assays confirmed that commonly used nosZ-targeted primer sets including Nos661F/Nos1773R (52), NosZ-F/nosZ1622R (51, 53), nosZ1F/nosZ1R, and nosZ2F/nosZ2R (49) are not comprehensive and fail to amplify the atypical nosZ genes.”
Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland (2006, background): “(22) under the same conditions as those described for the nirK primers (6).”
Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis (2007, background): “, 1998), denitrifying genes (Throback et al., 2004), ammonia monooxygenase (Avrahami et al.”
Past, present and future of soil quality indices : A biological perspective (2008, background): “However, the problem of these studies is that they do not provide information about the function of microorganisms' species in soil (Throback et al., 2004).”