Denitrification Activity and Relevant Bacteria Revealed by Nitrite Reductase Gene Fragments in Soil of Temperate Mixed Forest

Abstract

Denitrification activity and bacterial community constituents were investigated in both well-drained and poorly drained soils of a temperate forest in central Japan by 15 N tracer experiments and a cloning-sequencing approach. Denitrification activity was much higher in wet soil than in dry soil, based on 15 N 15 N ( 30 N 2 ) and 15 N 15 NO ( 46 N 2 O) production. Labeled nitrate ( 15 NO 3 − ) was immediately reduced to 30 N 2 in wet soil, whereas it was only reduced to 46 N 2 O in dry soil. Thus, the wet soil at the lower end of the catchment is a functional site for the scavenging for NO 3 − and N 2 O. Nitrite reductase gene (nirK and nirS) fragments from these soils were PCR amplified, cloned, and sequenced. Both nirK and nirS fragments were detected in the wet soil, whereas only nirK fragments were detected in the dry soil. All the nirK and nirS clones showed less than 90% similarity to known clones. Numerous operational taxonomic units for nirK and nirS were found in the wet soil. Considerable diversification within the largest clade on the nirK phylogenetic tree, which contained no known sequence, was observed in wet soil. Thus, a wet soil environment can provide both the habitat and conditions for the expression of denitrification activity.

N₂O Emission from Degraded Soybean Nodules Depends on Denitrification by <i>Bradyrhizobium japonicum</i> and Other Microbes in the Rhizosphere

“…Prokaryotic denitrification, fungal denitrification, ammonium oxidation, and nitrate ammonification have been nominated as soil microbial sources of N 2 O (1, 14, 26, 38, 49, 50, 57). Community analysis specific to degrading nodules that emit N 2 O found many microorganisms that potentially produce N 2 O (20), including denitrifying bacteria such as Acidovorax (19) and Enterobacter (2); Bradyrhizobium (25), Salmonella (48), Xanthomonas (52), and Pseudomonas (36), which have functional genes and/or activities for denitrification; and Fusarium , a denitrifying fungus (45).…”

Ecological Perspectives on Microbes Involved in N-Cycling

“…Hawkes et al (36) showed that changes in the gross nitrification rate along with changes in the plant community after exotic plant invasion in grasslands could be explained by the population size of AOB. The basic concept linking microbial community dynamics with N biogeochemistry apply to the majority of other dissimilating processes in N-cycling, including N-fixation, nitrite oxidation, denitrification, N 2 O reduction, and anammox (5, 38, 43, 58, 67, 100, 135). Spatial variations in N 2 O/N 2 emission potential in a grassland pasture can be described using spatial variations in the relative abundance of nirS and nirK in denitrifiers to nosZ in denitrifiers and non-denitrifies (93).…”

Biogeochemistry of nitrous oxide in groundwater in a forested ecosystem elucidated by nitrous oxide isotopomer measurements

“…1a. Katsuyama et al (2008) reported denitrification activities of surface soils collected from the area near SG1 (254-505 nmol N/g dry soil/h) and the groundwater collected from SG1-250 (from 1.4 Â 10 À4 to 1.7 Â 10 À3 nmol N 2 /ml/h). In addition, Koba et al (1997) examined the concentration and d 15 N of NO 3 À in soil solutions collected in the SG1 area and found the occurrence of denitrification with response to the precipitation.…”