Nitrous Oxide Reductase ( nosZ ) Gene Fragments Differ between Native and Cultivated Michigan Soils

Abstract

The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are ␣-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in ␥-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D mean ‫؍‬ 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D mean ‫؍‬ 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.

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

“…It has been reported that the addition of heavy metals or organic pollutants could decrease microbial diversity (Shannon index and richness) (Bamborough and Cummings, 2009;Kozdrój and van Elsas, 2001). The two diversity indices for nirK gene in our study were similar to those reported in forest soils and a paddy soil (Katuyama et al, 2008;Yoshida et al, 2009), and those of nosZ gene were similar to those reported in meadow and turfgrass soil (Dell et al, 2010;Stres et al, 2004;Zhang et al, 2006). However, the diversity indices for nirS gene in our study were lower than those in a flooded paddy field reported by Yoshida et al (2009).…”

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

“…This is consistent with observations that nosZ genotypes were more distinct between sites, while nifH genotypes were more likely to be shared across sites, differing mainly in their abundance. NosZ genotypes are known to exhibit high habitat specificity (Rö sch et al, 2002;Rich et al, 2003;Rich and Myrold, 2004;Stres et al, 2004), with few genotypes shared between sites with different C:N, pH, dominant vegetation and N availability (Rich et al, 2003). Experiments using other denitrification gene markers confirm that denitrifier gene communities tend to be unique to the environment from which they are sampled, with few genotypes shared between locations (Braker et al, 2000(Braker et al, , 2001.…”

“…Brodie et al (2002) and Stres et al (2004), based upon bacterial communities in disturbed grassland and upon denitrifiers in forest soils, respectively, claim that plant uniformity and higher pH seem to be more consistent factors associated with high microbe diversity than site vegetation. This was not supported at CH or RW.…”

Mitigation of postharvest nitrous oxide emissions from soybean ecosystems: a review

“…Furthermore, nosZ is found in various microbes in many environmental ecosystems. Previous studies showed that the activity and composition of soil microbes with nosZ are influenced by soil type and management (Stres et al 2004;Enwall et al 2005). Thus, the mitigation of N 2 O using nosZ must be thoroughly studied in the future to maximize its global potential.…”