Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems

Hu, Hang‐Wei; Macdonald, Catriona A.; Trivedi, Pankaj; Holmes, Bronwyn H.; Bodrossy, Levente; Singh, Brajesh K.

doi:10.1111/1462-2920.12481

Cited by 116 publications

(79 citation statements)

References 61 publications

(106 reference statements)

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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%

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%

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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“…Soil DNA extracts were stored at −80°C. Quantification of amoA for AOB and AOA were determined using amoA1f/amoA2r (Rotthauwe et al 1997) and crenamoA23f/crenamoA616r (Hu et al 2015), respectively. PCR reactions were conducted on a CFX96 (Bio-rad, USA).…”

Section: Dna Extraction and Quantitive Pcr (Qpcr) Analysesmentioning

confidence: 99%

“…The traditional viewpoint that soil ammonia oxidation and associated N 2 O emission is exclusively carried out by AOB has been challenged by the discovery of amoA and nirK genes in AOA strains (Venter et al 2004;Lund et al 2012) and by the demonstration of the N 2 O production capacity of AOA enriched or isolated from arable soils and marine ecosystem (Jung et al 2011(Jung et al , 2014Santoro et al 2011;Loscher et al 2012). In most soils, AOA outnumbers AOB abundance, a common feature in multiple ecosystems (Leininger et al 2006;He et al 2007;Hu et al 2013), and a high AOA ammonia oxidation activity has been assessed in certain soils (Yao et al 2011;Zhang et al 2012;Hu et al 2015). These results suggested that AOA could play a greater role than AOB in ammonia oxidation and N 2 O production in some soils (Nicol et al 2008;Stieglmeier et al 2014;Hink et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils

et al. 2016

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Nitrification is believed to be one of the major sources of N 2 O production emitted from soil. Previous studies showed that both ammonia-oxidising bacteria (AOB) and archaea (AOA) can produce N 2 O via nitrification but their relative contributions are still poorly defined. Here, we used acetylene, an inhibitor of AOB and AOA ammonia monooxygenase (AMO), and 1-octyne, a selective inhibitor that specifically inhibits AOB AMO, to investigate how AOB versus AOA contribute to N 2 O emissions in two distinct arable soils. Soil amended with ammonium (NH 4 + ) increased N 2 O emissions to a greater extent than nitrate (NO 3 − ), and acetylene had a greater impact on N 2 O emissions in NH 4 + -treated soils than that in NO 3 − -amended soils, which indicated that nitrification was the dominant N 2 O emitting process in these two arable soils. In the alluvial and red soil, the percentage of evolved N 2 O after application of NH 4 + by AOB were 70.5~78.1 % and 18.7~19.7 % by AOA, respectively. Quantitative PCR revealed that NH 4 + addition stimulated AOB growth, and the growth could be significantly inhibited by acetylene or 1-octyne in the two soils. The stimulation of N 2 O emissions by NH 4 + and the relative suppression by inhibitors paralleled fluctuations in the AOB growth. In addition, cumulative N 2 O emissions were not correlated with AOA abundance in the two soils. Our results revealed that AOB could contribute more to soil N 2 O production than AOA in the NH 4 + -amended arable soils.

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“…Digests were incubated at 37 • C for 3 h, followed by 10 min at 95 • C to deactivate the restriction enzyme. Terminal restriction fragments (TRFs) were resolved on an ABI PRISM 3500 Genetic Analyzer (Applied Biosystems, CA, USA), and processed using Genemapper version 4.0 (Applied Biosystems) as described previously (Hu et al 2015(Hu et al , 2016. The relative fluorescence abundance of all TRFs was exported for downstream analysis.…”

Section: Community Profiling Of the Bacterial 16s Rrna Gene By Terminmentioning

confidence: 99%

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

Han

Shi

et al. 2015

FEMS Microbiology Ecology

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107

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One sentence summary: The study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Editor: Kornelia Smalla ABSTRACTThe emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

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Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems

Cited by 116 publications

References 61 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

Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

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