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

Katsuyama, Chie; Kondo, N; Suwa, Yuichi; Yamagishi, Takao; Itoh, Masatoshi; Ohte, Nobuhito; Kimura, Hiroyuki; Nagaosa, Kazuyo; Kato, Kenji

doi:10.1264/jsme2.me08541e

Cited by 15 publications

(21 citation statements)

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“…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).…”

Section: Shifts In Diversity and Composition Of The Denitrifying Commsupporting

confidence: 86%

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

Guo

Deng

Qiao

et al. 2011

Environmental Pollution

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a b s t r a c tToxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0e500 mg kg À1 ) followed by doseeresponse and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC 50 values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC 50 concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.

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Section: Shifts In Diversity and Composition Of The Denitrifying Commsupporting

confidence: 86%

“…Phylogenetic analysis was performed using a neighbor-joining algorithm and distance calculation by MEGA4. Sequences that were 95% or more identical were considered as a unique operational taxonomic unit (OTU) (Katuyama et al, 2008).…”

Section: Cloning Sequencing and Phylogenetic Analysismentioning

confidence: 99%

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

Guo

Deng

Qiao

et al. 2011

Environmental Pollution

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“…By subtracting the amount of N2O from the combined amounts of N2O and N2, we can estimate the amount of N2. We used this approach because it is difficult to directly measure the amount of N2 by conventional gas chromatography (15). The proportion of N2 in the denitrification end products was calculated as N2/(N2+N2O).…”

Section: Proportion Of N2 In the Denitrification End Productsmentioning

confidence: 99%

Phylogenetic and Functional Diversity of Denitrifying Bacteria Isolated from Various Rice Paddy and Rice-Soybean Rotation Fields

et al. 2011

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Denitrifiers can produce and consume nitrous oxide (N2O). While little N2O is emitted from rice paddy soil, the same soil produces N 2 O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N 2 in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N 2 -producing denitrifiers.

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“…Furthermore, as demonstrated by Jones et al (2008), these nirK and nirS sequences were not considered during the design and modification of the nirK and nirS primers described above. However, even after the report of Jones et al (2008), the conventional primers are still widely used to illustrate the ecological traits of denitrifying microorganisms in the environment (for example, Katsuyama et al, 2008;Yoshida et al, 2012;Li et al, 2014). This suggests that the diversity, abundance and functional importance of denitrifying microorganisms in the environment are underestimated at present.…”

Section: Introductionmentioning

confidence: 99%

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

et al. 2015

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Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2-6 times more abundant than those revealed with the conventional primers. RNA-and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.

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

Cited by 15 publications

References 0 publications

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

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

Phylogenetic and Functional Diversity of Denitrifying Bacteria Isolated from Various Rice Paddy and Rice-Soybean Rotation Fields

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

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