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

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