Document Type
Article
Department/Program
Virginia Institute of Marine Science
Publication Date
2015
Journal
Fems Microbiology Ecology
Volume
91
Issue
2
Abstract
Microorganisms are capable of producing N-2 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.
DOI
10.1093/femsec/fiu004
Keywords
Ammonia-Oxidizing Archaea; Denitrifying Bacterial Communities; Nitrous-Oxide Production; Nitrosomonas-Europaea; N2O-Producing Pathways; Molecular Diversity; Nitrate Reducers; Genome Sequence; Paddy Soil; Denitrification
Recommended Citation
Long, A; Song, BK; Fridey, K; and Silva, A, Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils (2015). Fems Microbiology Ecology, 91(2).
10.1093/femsec/fiu004
