Changes in Bacterial Denitrifier Community Abundance over Time in an Agricultural Field and Their Relationship with Denitrification Activity

Dandie, Catherine E.; Burton, David L.; Zebarth, Bernie J.; Henderson, Sherri L.; Trevors, J. T.; Goyer, Claudia

doi:10.1128/aem.00441-08

Cited by 136 publications

(112 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The abundance of nosZ gene was the highest one among the three functional genes in this study. This result was higher than those of previously reported: nosZ density of 3×10 6 -2.8×10 8 copies g −1 dry soil (Kandeler et al 2006;Dandie et al 2008;Hallin et al 2009). But Chronakova et al (2009) found the nosZ gene copy number was in a range of 9.1×10 7 -7.5×10 9 copies g −1 soil in an upland pasture soil.…”

Section: Abundances Of Nirs Nirk and Nosz Genes Under Different Irrcontrasting

confidence: 73%

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Zhou

Zheng

Shen

et al. 2011

Environ Sci Pollut Res

View full text Add to dashboard Cite

Purpose Denitrification is an important biochemical process in global nitrogen cycle, with a potent greenhouse gas product N 2 O. Wastewater irrigation can result in the changes of soil properties and microbial communities of agricultural soils. The purpose of this study was to examine how the soil denitrification genes responded to different irrigation regimes. Materials and methods Soil samples were collected from three rural districts of Beijing (China) with three different irrigation regimes: clean groundwater (CW), reclaimed water (RW), and wastewater (WW). The abundance and diversity of three denitrification microbial genes (nirS, nirK, and nosZ) were examined by real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) molecular approaches. Results and discussion The abundance of nirS in the WW treatment was higher than that in the CW treatment, and no significant difference was found between the RW and CW or WW treatments. The abundance of nirK gene of the RW and WW treatments was higher than that of the CW treatment. There was no difference for nosZ gene among the three treatments. Correspondence analysis based on the DGGE profiles showed that there was no obvious difference in the nosZ gene composition, but nirS and nirK genes changed with different irrigation regimes. Conclusions Irrigation with unclean water sources enhanced the soil NO 3 − content and changed the abundance and composition of soil denitrifiers, and different functional genes had different responses. Irrigation with unclean water sources increased the abundance of nirK gene and changed the community structures of nirS and nirK genes, while nosZ gene was relatively stable in the soil. These results could be helpful to explore the mechanisms of the variation of denitrification processes under long-term wastewater irrigation and partially explain the reason of more N 2 O output in the field with wastewater irrigation.

show abstract

Section: Abundances Of Nirs Nirk and Nosz Genes Under Different Irrcontrasting

confidence: 73%

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Zhou

Zheng

Shen

et al. 2011

Environ Sci Pollut Res

View full text Add to dashboard Cite

show abstract

“…As assessed by quantitative PCR methods, the abundance of denitrifying bacteria was reported to be 10 5 to 10 9 g −1 upland soil (9,14,16,17,37) and 10 6 to 10 7 g −1 paddy soil (45,46). These counts appear to be lower than the results obtained in the present study by direct in situ PCR.…”

contrasting

confidence: 56%

Visualization and Direct Counting of Individual Denitrifying Bacterial Cells in Soil by nirK-Targeted Direct in situ PCR

et al. 2011

View full text Add to dashboard Cite

The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10 8 to 2.6 × 10 9 cells g −1 dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.

show abstract

“…Although the present study was useful in understanding the effect of NO 3 Ϫ on cnorB gene expression in P. mandelii culture with or without NO 3 Ϫ addition, the effect of different NO 3 Ϫ concentrations, including intermediate NO 3 Ϫ concentrations on cnorB, nirS, and nosZ denitrification genes, was not addressed. Many denitrification studies use the acetylene inhibition method to measure short-term denitrification activity in soil (6,11,15,17,18,20,23) and pure cultures (3,19,25). Acetylene blocks the action of nitrous oxide reductase enzyme, thereby inhibiting the reduction of N 2 O to N 2 (3,12,25).…”

mentioning

confidence: 99%

Effect of Nitrate and Acetylene on nirS , cnorB , and nosZ Expression and Denitrification Activity in Pseudomonas mandelii

Saleh-Lakha

Shannon

Henderson

et al. 2009

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Nitrate acts as an electron acceptor in the denitrification process. The effect of nitrate in the range of 0 to 1,000 mg/liter on Pseudomonas mandelii nirS, cnorB, and nosZ gene expression was studied, using quantitative reverse transcription-quantitative PCR. Denitrification activity was measured by using the acetylene blockage method and gas chromatography. The effect of acetylene on gene expression was assessed by comparing denitrification gene expression in P. mandelii culture grown in the presence or absence of acetylene. The higher the amount of NO 3 ؊ present, the greater the induction and the longer the denitrification genes remained expressed. nirS gene expression reached a maximum at 2, 4, 4, and 6 h in cultures grown in the presence of 0, 10, 100, and 1,000 mg of KNO 3 /liter, respectively, while induction of nirS gene ranged from 12-to 225-fold compared to time zero. cnorB gene expression also followed a similar trend. nosZ gene expression did not respond to NO 3 ؊ treatment under the conditions tested. Acetylene decreased nosZ gene expression but did not affect nirS or cnorB gene expression. These results showed that nirS and cnorB responded to nitrate concentrations; however, significant denitrification activity was only observed in culture with 1,000 mg of KNO 3 /liter, indicating that there was no relationship between gene expression and denitrification activity under the conditions tested.

show abstract

Changes in Bacterial Denitrifier Community Abundance over Time in an Agricultural Field and Their Relationship with Denitrification Activity

Cited by 136 publications

References 35 publications

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Visualization and Direct Counting of Individual Denitrifying Bacterial Cells in Soil by nirK-Targeted Direct in situ PCR

Effect of Nitrate and Acetylene on nirS , cnorB , and nosZ Expression and Denitrification Activity in Pseudomonas mandelii

Contact Info

Product

Resources

About