Direct seeding mulch-based cropping increases both the activity and the abundance of denitrifier communities in a tropical soil

Baudoin, Ezékiel; Philippot, Laurent; Chèneby, Dominique; Chapuis‐Lardy, Lydie; Fromin, Nathalie; Bru, David; Rabary, Bodovololona; Brauman, Alain

doi:10.1016/j.soilbio.2009.05.015

Cited by 56 publications

(56 citation statements)

References 42 publications

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“…Several soil properties other than pH were also affected by the addition of acid or alkali solutions. For example, the NH 4 ϩ concentration was higher in the acidic soil than in the natural pH and alkaline soils, while the NO 3 Ϫ concentration was higher in the soils with alkaline pH and decreased significantly with decreasing pH (Tukey HSD test, P Ͻ 0.05). The microbial biomass determined by the fumigation extraction method (C mic ) was lowest in the acidic soils and highest in the alkaline soils (Tukey HSD test, P Ͻ 0.05).…”

mentioning

confidence: 97%

“…Denitrification is the microbial reduction of NO 3 Ϫ via NO 2 Ϫ to gaseous NO, N 2 O, and N 2 , which are then lost into the atmosphere (36). It therefore results in considerable loss of nitrogen, one of the most limiting nutrients for crop production in agriculture (20).…”

mentioning

confidence: 99%

“…The gas samples were stored in evacuated (Ͻ100 Pa), septum-capped, 12-ml vials (Labco), and the concentration and 15 N content of N 2 O and the 15 N content of the N 2 in each 12-ml vial were determined by automated isotope ratio mass spectroscopy as described by Stevens et al (48), using a Europa Scientific 20-20 stable-isotope analyzer interfaced with a Europa Scientific ANCA-TG trace gas preparation system (Europa (31). The total N fluxes during the 74-h period after the application of 15 N-labeled KNO 3 were calculated by integration, assuming a linear change in flux rates between observation times.…”

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confidence: 99%

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Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity

Čuhel

Šimek

Laughlin

et al. 2010

Appl Environ Microbiol

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401

182

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The objective of this study was to investigate how changes in soil pH affect the N 2 O and N 2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H 2 SO 4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N 2 O and N 2 emissions using the 15 N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N 2 O/(N 2 O ؉ N 2 ) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N 2 O production were observed. Denitrification activity and N 2 O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N 2 O/(N 2 O ؉ N 2 ) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.Denitrification is the microbial reduction of NO 3 Ϫ via NO 2 Ϫ to gaseous NO, N 2 O, and N 2 , which are then lost into the atmosphere (36). It therefore results in considerable loss of nitrogen, one of the most limiting nutrients for crop production in agriculture (20). Denitrification is also of environmental concern since, together with nitrification, it is the main biological process responsible for N 2 O emissions (7). N 2 O is a potent greenhouse gas which has a global warming potential about 320 times greater than that of CO 2 and has a lifetime of approximately 120 years (32). In the stratosphere, N 2 O can also react with O 2 to produce NO, which induces the destruction of stratospheric ozone (8). N 2 O can be released into the atmosphere by incomplete denitrification due to the effect of environmental conditions on the regulation of the different denitrification reductases (14, 41, 51), but it has recently been suggested that it could also be due to lack of nitrous oxide reductase in some denitrifiers (19,41). Since N 2 O is an intermediate in the denitrification pathway, both the amount of N 2 O produced and the N 2 O/(N 2 O ϩ N 2 ) ratio are important in understanding and predicting N 2 O fluxes from soils. The main environmental factors known to influence the N 2 O/(N 2 O...

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confidence: 97%

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confidence: 99%

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confidence: 99%

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Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity

Čuhel

Šimek

Laughlin

et al. 2010

Appl Environ Microbiol

Self Cite

401

182

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“…In many laboratories, utilization of commercial kits for DNA isolation is also frequent. Among them are MoBIO PowerSoil DNA kit (MoBIO) [19,24,62], ultra clean soil DNA kit (Ozyme, MoBIO) [5,61,99], and fast DNA spin kit for soil (BIO 101/Q-Biogene) [29,50,55,102].…”

Section: Other Extraction and Purification Methodsmentioning

confidence: 99%

“…Primers used for amplification are presented in Table 1. Those primers have been used for amplification of the 16S rRNA and denitrification genes from agricultural soils [1,5,23,62,72], forest soils [4], containers filled with wood byproducts [128], rice paddy field soils [134], grassland pasture soils [82], soils from the Burgundy region [10], soil-feeding mounds of nematodes [28], technosols [40], and constructed wetlands [21].…”

Section: Preparation Of Standard Dnas For Qpcrmentioning

confidence: 99%

Determination of Denitrification Genes Abundance in Environmental Samples

Correa‐Galeote¹,

Tortosa²,

Bedmar³

2013

Metagenomics

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Diversity of microorganisms involved in the biogeochemical N cycle is of fundamental interest in microbial ecology. Denitrification is a key step in the cycle by which nitrate is reduced to dinitrogen gas via the soluble nitrite and the gaseous compounds nitric oxide and nitrous oxide. The process is carried out by the sequential activity of the nitrate, nitrite, nitric oxide, and nitrous oxide reductase enzyme, respectively. The fluorescence-based quantitative real-time polymerase chain reaction (qPCR) is widely used for quantification of nucleic acids in samples obtained from numerous, diverse sources. Here, we provide a well-proven methodology for isolation of DNA from environmental samples and describe relevant experimental conditions for utilization of qPCR to assay the 16S rRNA and nar/nap, nirK/nirS, c-nor/qnor, and nos denitrification genes that encode synthesis of denitrifying enzymes. The ISO 11063 standard method and MIQUE guidelines are considered with the aim to increase experimental transparency.

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The mechanisms governing low denitrification capacity and high nitrogen oxide gas emissions in subtropical forest soils in China

Zhang

Zhu

et al. 2014

J. Geophys. Res. Biogeosci.

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Previous studies have demonstrated that denitrification rates are low in subtropical forest soils.However, the mechanisms governing this process are not well known. This study seeks to identify the mechanisms responsible for the low denitrification capacity and high nitrogen oxide gas ratio in subtropical forest soils in China. The denitrification capacity and nitric oxide (NO), nitrous oxide (N 2 O), and dinitrogen (N 2 ) emission rates were measured using the acetylene inhibition method under conditions of added nitrate and anoxia. The abundance of nitrate reductase (narG), nitrite reductase (nirK), nitric oxide reductase (cnorB), and nitrous oxide reductase (nosZ) was measured using real-time, quantitative polymerase chain reaction, and sequencing of the nirK and norB products was performed to analyze the population structure of denitrifying bacteria. These results showed that the denitrification capacity in subtropical forest soils was lower than in temperate forest soils (p < 0.05). Multiple regression analysis showed that redox potential at the start of incubation (Eh i ), rather than soil pH or soil organic C, was the key soil variable influencing denitrification, and Eh i alone could explain 68% of the variations in denitrification capacity. The high Eh i in subtropical soils led to a low abundance of nirK and significant differences in the population structure of denitrifying bacteria between subtropical and temperate soils. Therefore, Eh i was responsible for the low denitrification capacity in subtropical forest soils. The ratio of NO to total denitrification gas products (p < 0.01) and the ratio of NO and N 2 O to total denitrification gas products (p < 0.05) were significantly higher in subtropical forest soils than in temperate forest soils, while the reverse trend was observed for the ratio of N 2 to total denitrification gas products (p < 0.05). A high Eh i reduced the specific reduction activity of each nosZ copy and, in turn, resulted in a large ratio of NO and N 2 O to total denitrification gas products in subtropical soils. Thus, NO and N 2 O, but not N 2 , were the dominant denitrification gas products, accounting for 80%, even under the highly anaerobic conditions in subtropical forest soils and despite low denitrification capacity. These results were significant for understanding the "Hole in the Pipe" model and NO and N 2 O gases emission in subtropical forest soils. Despite the fact that the nitrogen flowing through the pipe (denitrification capacity) was low, the large holes in the pipe resulted in a large quantity of NO and N 2 O gases leaking out. This leakage may be a potential mechanism for the high levels of NO and N 2 O gas emission in subtropical forest soils and could partly explain why NO and N 2 O emissions are generally high in subtropical and tropical soils.

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Direct seeding mulch-based cropping increases both the activity and the abundance of denitrifier communities in a tropical soil

Cited by 56 publications

References 42 publications

Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity

Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity

Determination of Denitrification Genes Abundance in Environmental Samples

The mechanisms governing low denitrification capacity and high nitrogen oxide gas emissions in subtropical forest soils in China

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Direct seeding mulch-based cropping increases both the activity and the abundance of denitrifier communities in a tropical soil

Cited by 56 publications

References 42 publications

Insights into the Effect of Soil pH on N 2 O and N 2 Emissions and Denitrifier Community Size and Activity

Insights into the Effect of Soil pH on N 2 O and N 2 Emissions and Denitrifier Community Size and Activity

Determination of Denitrification Genes Abundance in Environmental Samples

The mechanisms governing low denitrification capacity and high nitrogen oxide gas emissions in subtropical forest soils in China

Contact Info

Product

Resources

About

Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity

Insights into the Effect of Soil pH on N ₂ O and N ₂ Emissions and Denitrifier Community Size and Activity