Community composition and activities of denitrifying bacteria from adjacent agricultural soil, riparian soil, and creek sediment in Oregon, USA

Rich, Jeremy J.; Myrold, David D.

doi:10.1016/j.soilbio.2004.03.008

Cited by 120 publications

(82 citation statements)

References 34 publications

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…Although changes in nitrate availability often exert only short-term effects on the denitrifier community, an increase in this substrate has been shown to decrease denitrifier abundance (Wallenstein et al, 2006). It is known that experimental nutrient amendments increase the rates of N 2 O production (Avrahami et al, 2002;Seitzinger et al, 2006), but it still has not been confirmed if denitrifying enzyme activity is correlated with the genetic structure of denitrifier communities (Rich and Myrold, 2004;Boyle et al, 2006;Sharma et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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

2008

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Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

2008

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“…Across all soil samples, total T-RF richnesses were nirS = 52, nirK = 53, nosZ = 47, which are typical values for T-RFLP studies of functional genes in soils (Deslippe et al, 2014;Rich and Myrold, 2004;Rösch and Bothe, 2005). While the minimum and maximum numbers of T-RFs varied among samples, the patterns of richness, evenness, and diversity among soils belonging to the three groups of soils were similar (see Table S4).…”

Section: Bacterial Denitrifiers In New Zealand Dairy-grazed Pasture Smentioning

confidence: 72%

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

et al. 2017

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Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N 2 O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N 2 O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N 2 O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N 2 O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N 2 O emissions through denitrification across a wide range of soil types.

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“…However, in Müller et al (2002), DMPP did not affect NaR or N 2 O reductase capacity in a silty clay soil, even at concentrations 14 times higher than the recommended concentration. Several studies (Rich et al 2004, Boyle et al 2006 indicated that there were no obvious relationships between the activities of denitrifying enzymes and the abundance of denitrifiers in certain environments. Also, to date, there was no published evidence for the effects of NIs on denitrifiers.…”

Section: Results and Conclusionmentioning

confidence: 99%

“…Also, to date, there was no published evidence for the effects of NIs on denitrifiers. Soil environments such as nitrate content and water availability are two important factors affecting denitrifying activities in soil (Rich et al 2004). Tindaon et al (2011) indicated that denitrification potential was affected by the application of NIs at 10-50 times the recommended dose in various agricultural soils, owing to the inhibition of NO 3 -production.…”

Section: Results and Conclusionmentioning

confidence: 99%

The response of nitrifier, N-fixer and denitrifier gene copy numbers to the nitrification inhibitor 3,4-dimethylpyrazole phosphate

Dong¹,

Zhang²,

Wu³

et al. 2013

PLANT SOIL ENVIRON

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A laboratory incubation experiment was conducted to examine the effects of 3,4-dimethylpyrazole phosphate (DMPP) on the transformation of urea-N and associated microbial communities in a low-fertility brown soil. The soil was supplied with urea at 180 kg N/ha and DMPP at 0, 1.8 or 18 kg/ha, while soil that was not supplied with urea and DMPP was treated as the control. Soil mineral nitrogen (NH 4 + -N and NO 3 --N) was measured at regular intervals, and temporal variations in the population sizes of nitrogen-cycling microbes were determined using realtime PCR. Compared to the urea-alone treatment, the additional application of DMPP maintained significantly higher (P < 0.05) NH 4 + -N concentrations and lower NO 3 --N (P < 0.05) concentrations in the soil and decreased the population sizes of ammonia oxidizing and denitrifying microbes but promoted the growth of nitrogen-fixing bacteria. The results suggest that the application of DMPP is beneficial in improving the availability of fertilizer-N for plant uptake. This study is the first comprehensive investigation to examine the effects of DMPP on the functional microorganisms that are important in nitrogen-cycling processes.

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Community composition and activities of denitrifying bacteria from adjacent agricultural soil, riparian soil, and creek sediment in Oregon, USA

Cited by 120 publications

References 34 publications

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

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

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

The response of nitrifier, N-fixer and denitrifier gene copy numbers to the nitrification inhibitor 3,4-dimethylpyrazole phosphate

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