dAnammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N 2 gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N 2 in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N 2 production, molecular and 15 N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes, respectively, while the internal transcribed spacer (ITS) of Fusarium oxysporum was quantified to estimate the abundance of codenitrifying and denitrifying fungi.15 N tracer incubation experiments with 15 NO 3 ؊ or 15 NH 4 ؉ addition were conducted to measure the N 2 production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N 2 production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed by F. oxysporum based on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N 2 -N g ؊1 day ؊1 , while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N 2 -N g ؊1 day ؊1 . Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N 2 production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle. The application of inorganic nitrogen fertilizers in agricultural fields causes various environmental problems, including eutrophication and habitat degradation. Accurate quantification of the processes removing fixed nitrogen is increasingly important to gain a better understanding of the fate of nitrogen in agricultural soils. Three microbial processes, denitrification, codenitrification, and anaerobic ammonium oxidation (anammox), are involved in the removal of nitrogen from soils through the production of nitrous oxide (N 2 O) or dinitrogen gas (N 2 ) (1, 2). Denitrification is a microbial process in which nitrate (NO 3 Ϫ ) and nitrite (NO 2 Ϫ ) are converted to N 2 O and N 2 in aerobic and anaerobic soils. It is a well-studied process in bacteria and has recently been found to occur in archaea and fungi (3). Codenitrification produces N 2 O and N 2 through the reduction of nitrite (NO 2 Ϫ ) by other nitrogen compounds, including azide, ammonium (NH 4 ϩ ), salicylhydroxamic acid, and hydroxylamine (4, 5). Codenitrification can occur in both fungi (e.g., Fusarium oxysporum) and bacteria (e.g., Streptomyces antibioticus) (5, 6) and has been measured in grassland and agricultural soils (4, 7). Fungal codenitrification...

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.

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