Diversity of Nitrite Reductase ( nirK and nirS ) Gene Fragments in Forested Upland and Wetland Soils

Abstract

The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one pattern was found in both soils and in each soil two dominant groups comprised >35% of all clones. No dominance and few redundant patterns were seen among the nirS clones. Phylogenetic analysis of deduced amino acids grouped the nirK sequences into five major clusters, with one cluster encompassing most marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall, the data indicated that the denitrifying communities in the two soils have many members and that the soils have a high richness of different nir genes, especially of the nirS gene, most of which have not yet been found in cultivated denitrifiers.

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

“…nirS diversity is higher than nirK diversity in some aquifers, marsh and costal sediments, suggesting that (semi-)aquatic systems sustain diverse nirS-type denitrifiers (Braker et al, 2000;Prieme et al, 2002;Santoro et al, 2006). Such findings are in agreement with the high detected nirS diversity in acidic peat soils (Table 4).…”

“…Organisms hosting both types of nitrite reductase are unknown to date (Heylen et al, 2006). The genes coding for the above-named oxidoreductases are commonly used as structural gene markers for the analysis of nitrate reducer and denitrifier communities (Braker et al, 2000;Philippot et al, 2002;Prieme et al, 2002;Rich et al, 2003;Horn et al, 2006;Enwall et al, 2010;Jones and Hallin, 2010;Palmer et al, 2010;Bru et al, 2011). The main products of denitrification that are released into the atmosphere are N 2 or N 2 O. Denitrifiers might lack nitrate reductases and/or N 2 O reductases, and occupy diverse ecological niches (Tiedje, 1988;Zumft, 1997;Shapleigh, 2006).…”

Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

“…Virtually nothing is known about the environmental preferences of denitrifying bacteria (Prieme et al 2002). According to our results from T-RFLP and clone libraries, the diversity of denitrifying communities carrying nirS or nirK varies at different depths of the water column of Lake Kinneret.…”

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils

“…Richness of nosZ genotypes also declined significantly with warming. A marshy site such as SM might have been expected to have higher overall denitrifier richness (Priemé et al, 2002), but the richness was comparable to the UG site, which also had a more acidic pH, so this may have limited nosZ diversity.…”