title: Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils.
abstract: Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.
authors.affiliation: Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403.
authors.forename: Andrew
authors.initials: A
authors.lastname: Long
authors.affiliation: Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403 Department of Biological Sciences, Virginia Institute of Marine Sciences, Gloucester Point, VA 23062, USA Department of Life Science, Dongguk University-Seoul, Seoul 100-715, South Korea songb@vims.edu.
authors.forename: Bongkeun
authors.initials: B
authors.lastname: Song
authors.affiliation: Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403.
authors.forename: Kelly
authors.initials: K
authors.lastname: Fridey
authors.affiliation: Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403.
authors.forename: Amy
authors.initials: A
authors.lastname: Silva
mesh_terms: D000383:Agriculture; D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology* / Q000235:genetics; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D001483:Base Sequence; D003300:Copper / Q000378:metabolism; D017931:DNA Primers / Q000235:genetics*; D058440:Denitrification; D005658:Fungi / Q000201:enzymology* / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D008969:Molecular Sequence Data; D009572:Nitrite Reductases / Q000235:genetics* / Q000378:metabolism; D009573:Nitrites / Q000737:chemistry; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012987:Soil; D012988:Soil Microbiology
chemical_list: D017931:DNA Primers; D009573:Nitrites; D012987:Soil; D003300:Copper; D009572:Nitrite Reductases; C052695:nitrite reductase, copper-containing
keywords: archaea; denitrification; fungi; nirK; nitrification