Nitrous oxide reductase ( nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments

• Published in: FEMS microbiology letters 1998-05, Vol.162 (1), p.61-68
• Main Authors: Scala, David J, Kerkhof, Lee J
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacteriological methods and techniques used in bacteriology; Bacteriology; Base Sequence; Biological and medical sciences; Cloning, Molecular; DNA Primers; DNA, Bacterial - analysis; DNA, Bacterial - genetics; Fundamental and applied biological sciences. Psychology; Genes, Bacterial - genetics; Geologic Sediments - microbiology; Gram-Negative Aerobic Bacteria - genetics; Marine sediment; Microbiology; Molecular Sequence Data; Nitrous oxide reductase; nosZ; Oxidoreductases - genetics; PCR primer; Phylogeny; Polymerase Chain Reaction - methods; Sequence Alignment; Sequence Analysis, DNA
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1016/S0378-1097(98)00103-7

Two PCR primer sets for the nitrous oxide reductase gene ( nosZ) were developed. The initial primers were based on three sequences in GenBank and used to amplify nosZ from continental shelf sediments and from two denitrifiers in culture, Thiosphaera pantotropha and Pseudomonas denitrificans. Three unique marine sediment nosZ genes were identified and sequenced. The marine nosZ genes were most closely related to the nosZ genes of Paracoccus denitrificans or to Rhizobium meliloti. Alignment of all nosZ sequences currently available ( n=10) facilitated redesign of the PCR primers. Three new primer sets which amplify 1100 bp, 900 bp and 250 bp regions of the nosZ gene were designed and tested. The new primers robustly amplified nosZ fragments from samples in which the initial nosZ primers were only marginally successful.