Archaea rather than bacteria control nitrification in two agricultural acidic soils

Gubry‐Rangin, Cécile; Nicol, Graeme W.; Prosser, James I.

doi:10.1111/j.1574-6941.2010.00971.x

Cited by 363 publications

(242 citation statements)

References 52 publications

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“…7), which was in line with previous studies that group 1.1b might be more abundant in neutral and alkaline soils (Jia and Conrad 2009;Hu et al 2015), whereas group 1.1a had a higher ammonia affinity and preferred to live in acidic red soil (Gubry-Rangin et al 2010). T-RFLP and PCA analysis showed the AOA community structure remained relatively stable among the treatments (Fig.…”

Section: Aoa-otu7 (256bp)supporting

confidence: 91%

“…These compounds inhibit nitrification by deactivating ammonia monooxygenase (AMO) and blocking the growth of AOB and AOA (Di et al 2010a;Hink et al 2016). DCD or C 2 H 2 was reported to be more effective in inhibiting AOA compared with AOB in low-pH soils (Gubry-Rangin et al 2010;Zhang et al 2012), and vice verse in nitrogen-rich soils (Di et al 2009;Jia and Conrad 2009;Dai et al 2013;Chen et al 2015). Moreover, by comparing the inhibitory effects of different NIs on the growth of ammonia oxidizers using pure cultures, DCD exhibited a stronger inhibitory effect on AOB than AOA, while nitrapyrin dramatically inhibited the growth of AOA (Shen et al 2013).…”

Section: Introductionmentioning

confidence: 97%

“…In fact, archaeal amoA genes appear to be ubiquitously distributed in soils ) and they are more abundant than bacterial amoA genes in most terrestrial ecosystems (Leininger et al 2006;He et al 2007). A positive relationship between potential ammonia oxidation and archaeal amoA gene or transcript abundance, but not AOB, has been demonstrated in acidic soils (Gubry-Rangin et al 2010;Yao et al 2011;Zhang et al 2012), suggesting that ammoniaoxidizing archaea (AOA) may play a greater role than AOB in soil ammonia oxidation. However, the relative role of AOB and AOA in ammonia oxidation and N 2 O emission is not well understood.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Wang

Zhang

Shen

et al. 2016

Environ Sci Pollut Res

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Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N 2 O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C 2 H 2 ) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N 2 O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C 2 H 2 were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N 2 O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N 2 O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C 2 H 2 was more effective in reducing N 2 O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N 2 O emission and net nitrification rate, was more inhibited by C 2 H 2 than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C 2 H 2 ) could potentially alter N 2 O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.

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Section: Aoa-otu7 (256bp)supporting

confidence: 91%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Wang

Zhang

Shen

et al. 2016

Environ Sci Pollut Res

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“…Crenarchaeota include ammonia oxidizers and have been suggested to play important functional roles in carbon metabolism (Kemnitz, Kolb, & Conrad, 2007) and nitrogen cycling in soils (Gubry‐Rangin, Nicol, & Prosser, 2010; Schauss et al., 2009). They are known to respond positively to N addition (Leff et al., 2015), but here, we observed a negative correlation between their relative abundance and ammonia levels.…”

Section: Discussionmentioning

confidence: 99%

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

Reese

Lulow

David

et al. 2017

Ecology and Evolution

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Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic and abiotic conditions and microbial composition and diversity, there have been few experimental tests to determine the relative importance of these two sets of factors at local scales. Here, we report the results of a fully factorial experiment manipulating soil conditions and plant cover on old‐field mesocosms across a latitudinal gradient. The largest contributor to beta diversity was site‐to‐site variation, but, having corrected for that, we observed significant effects of both plant and soil treatments on microbial composition. Separate phyla were associated with each treatment type, and no interactions between soil and plant treatment were observed. Individual soil characteristics and biotic parameters were also associated with overall beta‐diversity patterns and phyla abundance. In contrast, soil microbial diversity was only associated with site and not experimental treatment. Overall, plant community treatment explained more variation than soil treatment, a result not previously appreciated because it is difficult to dissociate plant community composition and soil conditions in observational studies across gradients. This work highlights the need for more nuanced, multifactorial experiments in microbial ecology and in particular indicates a greater focus on relationships between plant composition and microbial composition during community assembly.

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“…Previous studies on the effects of soil pH on N 2 O emissions and/or ammonia-oxidising communities have been conducted in the laboratory (Thomsen et al 1994;Clough et al 2004;Bakken et al 2012) or on long term/natural soil pH plots (Weslien et al 2009;Gubry-Rangin et al 2010;Mahmood et al 2011;Zhang et al 2011). Few studies have determined the effect of soil pH change on N 2 O emissions, ammonia oxidising communities and DCD effectiveness in the field.…”

Section: Introductionmentioning

confidence: 99%

The effect of soil pH and dicyandiamide (DCD) on N2O emissions and ammonia oxidiser abundance in a stimulated grazed pasture soil

Robinson

Cameron

et al. 2014

J Soils Sediments

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Purpose Nitrous oxide (N 2 O) is a potent greenhouse gas which is mainly produced from agricultural soils through the processes of nitrification and denitrification. Although denitrification is usually the major process responsible for N 2 O emissions, N 2 O production from nitrification can increase under some soil conditions. Soil pH can affect N 2 O emissions by altering N transformations and microbial communities. Bacterial (AOB) and archaeal (AOA) ammonia oxidisers are important for N 2 O production as they carry out the ratelimiting step of the nitrification process. Material and methods A field study was conducted to investigate the effect of soil pH changes on N 2 O emissions, AOB and AOA community abundance, and the efficacy of a nitrification inhibitor, dicyandiamide (DCD), at reducing N 2 O emissions from animal urine applied to soil. The effect of three pH treatments, namely alkaline treatment (CaO/NaOH), acid treatment (HCl) and native (water) and four urine and DCD treatments as control (no urine or DCD), urine-only, DCD-only and urine + DCD were assessed in terms of their effect on N 2 O emissions and ammonia oxidiser community growth. Results and discussion Results showed that total N 2 O emissions were increased when the soil was acidified by the acid treatment. This was probably due to incomplete denitrification caused by the inhibition of the assembly of the N 2 O reductase enzyme under acidic conditions. AOB population abundance increased when the pH was increased in the alkaline treatment, particularly when animal urine was applied. In contrast, AOA grew in the acid treatment, once the initial inhibitory effect of the urine had subsided. The addition of DCD decreased total N 2 O emissions significantly in the acid treatment and decreased peak N 2 O emissions in all pH treatments. DCD also inhibited AOB growth in both the alkaline and native pH treatments and inhibited AOA growth in the acid treatment. Conclusions These results show that N 2 O emissions increase when soil pH decreases. AOB and AOA prefer different soil pH environments to grow: AOB growth is favoured in an alkaline pH and AOA growth favoured in more acidic soils. DCD was effective in inhibiting AOB and AOA when they were actively growing under the different soil pH conditions.

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Archaea rather than bacteria control nitrification in two agricultural acidic soils

Cited by 363 publications

References 52 publications

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

The effect of soil pH and dicyandiamide (DCD) on N2O emissions and ammonia oxidiser abundance in a stimulated grazed pasture soil

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