Community Composition and Functioning of Denitrifying Bacteria from Adjacent Meadow and Forest Soils

Abstract

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in ␣-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.

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

“…narG, nirK, nirS and nosZ were amplified using the primer pairs narG1960f (TAYGTSGGSCARGAR-AA)/narG2650r (TTYTCRTACCABGTBGC; Philippot et al, 2002), F1aCu (ATCATGGTSCTGCCGCG)/ R3Cu (GCCTCGATCAGRTTGTGGTT; Throbäck et al, 2004), cd3aF (GTSAACGTSAAGGARACSG G)/R3cd (GASTTCGGRTGSGTCTTGA; Throbäck et al, 2004) and nosZF (CGCTGTTCITCGACAGYC AG)/nosZR (ATGTGCAKIGCRTGGCAGAA; Rich et al, 2003), respectively. Each primer was preceeded by a 6-bp-long barcode (AGCGTC for unturbated and ATATAC for cryoturbated soil samples) to separate sequences after pyrosequencing.…”

“…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).…”

Identification and isolation of active N2O reducers in rice paddy soil

“…Therefore, it is difficult to use 16S rRNA gene sequences alone to identify N 2 O reducers. Instead, the gene encoding N 2 O reductase (nosZ) has been used to detect potential N 2 O reducers in various environments (Rich et al, 2003). Although nosZ phylogeny is generally in agreement with 16S rRNA gene phylogeny, horizontal gene transfer may have occurred among closely related microorganisms (Dandie et al, 2007;Jones et al, 2008) and we therefore cannot identify N 2 O reducers on the basis of nosZ sequence information alone.…”

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

“…The activity of reductases and the expression of functional genes involved in denitrification process varies among individual strains (Zumft, 1997), and community composition is thus considered to be able to influence functionality at both community and ecosystem levels (Braker et al, 2010). Nevertheless, some studies have reported correlations between abundance and function as well as between structure and function of denitrifying communities (Bremer et al, 2009;Hallin et al, 2009;Rich et al, 2003) while others not Miller et al, 2008;Wertz et al, 2009). Therefore, it is important to determine the correlations among changes in function, abundance and composition of the denitrifying community in an agricultural soil in response to PAHs stress.…”