AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: Aug. 4, 2017

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered be catalyzed by concerted activity ammonia- and nitrite-oxidizing microorganisms. Only recently, complete oxidizers ('comammox'), which oxidize nitrate on their own, were identified in bacterial genus Nitrospira, previously assumed contain only canonical oxidizers. Nitrospira are widespread nature, but for assessments distribution functional importance comammox ecosystems, cultivation-independent tools distinguish from strictly required. Here we developed new PCR primer sets that specifically target amoA genes coding subunit A distinct monooxygenase Nitrospira. While existing primers capture a fraction known diversity, cover as much 95% clade 92% B sequences reference database containing 326 with sequence information at binding sites. Application 13 samples engineered systems (a groundwater well, drinking water treatment wastewater plants) other habitats (rice paddy forest soils, rice rhizosphere, brackish lake sediment freshwater biofilm) detected all revealed considerable diversity most habitats. Excellent specificity was achieved avoiding use highly degenerate preparations using equimolar mixtures oligonucleotides match genes. Quantitative these sensitive specific, enabled efficient quantification gene copy numbers environmental samples. The measured relative abundances compared oxidizers, variable across environments. amoA-targeted enable more encompassing future studies nitrifying microorganisms diverse For example, they may used monitor population dynamics uncultured organisms under changing conditions response altered treatments agricultural ecosystems.

Language: Английский

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Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

Applied and Environmental Microbiology, Journal Year: 2014, Volume and Issue: 81(2), P. 745 - 753

Published: Nov. 15, 2014

Nitrification has an immense impact on nitrogen cycling in natural ecosystems and wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially nitrite-oxidizing bacteria (NOB) are lacking because a limited number pure cultures until recently. In this study, we compared nitrite oxidation kinetics six one enrichment culture representing three genera NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 27 μM nitrite, Nitrospira adapted live under significant substrate limitation. Nitrobacter showed wide range lower affinities, with Km values 49 544 nitrite. However, advantage emerged excess supply, sustaining high maximum specific activities (Vmax) 64 164 μmol nitrite/mg protein/h, contrary 18 48 protein/h. The Vmax (26 protein/h) (58 nitrite) "Candidatus Nitrotoga arctica" measured at low temperature 17°C suggest that can advantageously compete other NOB, cold habitats. determined represent improved basis for nitrifying will support predictions community structure nitrification rates engineered ecosystems.

Language: Английский

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Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle

Journal of Soils and Sediments, Journal Year: 2017, Volume and Issue: 17(12), P. 2709 - 2717

Published: Oct. 18, 2017

Language: Английский

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Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

The ISME Journal, Journal Year: 2014, Volume and Issue: 9(5), P. 1062 - 1075

Published: Oct. 10, 2014

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers nitrite under unique agricultural management is poorly understood. In this study, we report differential contributions ammonia-oxidizing archaea (AOA), bacteria (AOB) nitrite-oxidizing (NOB) to nitrification in four soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) Jia-Xing (JX)) that representative rice ecosystems China. urea-amended microcosms, activity varied greatly with 11.9, 9.46, 3.03 1.43 μg NO3(-)-N g(-1) dry weight soil per day ZY, JD, LZ JX soils, respectively, over course a 56-day incubation period. Real-time quantitative PCR amoA genes pyrosequencing 16S rRNA revealed significant increases AOA population various extents, suggesting their relative oxidation decreased ZY JD LZ. The opposite trend was observed for AOB, stimulated only AOB populations. DNA-based stable-isotope probing further demonstrated active numerically outcompeted bacterial counterparts 37.0-, 10.5- 1.91-fold (13)C-DNA whereas not AOA, were labeled during nitrification. NOB much greater extent than addition acetylene completely abolished assimilation (13)CO2 nitrifying Phylogenetic analysis suggested archaeal predominantly catalyzed fosmid 29i4-related within group 1.1b lineage. Nitrosospira cluster 3-like performed most majority (13)C-AOB affiliated Nitrosomona communis (13)C-NOB overwhelmingly dominated Nitrospira rather Nitrobacter. A correlation between AOA/AOB ratio capacity, implying advantage microaerophilic conditions. These results suggest important roles physiochemical properties determining activities oxidizers.

Language: Английский

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pH regulates key players of nitrification in paddy soils

Soil Biology and Biochemistry, Journal Year: 2014, Volume and Issue: 81, P. 9 - 16

Published: Nov. 16, 2014

Language: Английский

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Bacillus subtilis biofertilizer mitigating agricultural ammonia emission and shifting soil nitrogen cycling microbiomes

Environment International, Journal Year: 2020, Volume and Issue: 144, P. 105989 - 105989

Published: July 30, 2020

Excessive ammonia (NH3) emitted from nitrogen fertilizer application in farmland have caused serious disturbance to global environment, including reduction of visibility, formation regional haze, and increase deposition. Application biofertilizer has been considered as an effective approach for soil improvement agriculture sustainability. In this study, a field experiment was conducted evaluate the potential B. subtilis on mitigating NH3 volatilization investigate underlying mechanisms. Compared with organic fertilizer, incorporation reduced by up 44%. Moreover, abundance ureC gene, increased functional genes (bacterial amoA comammox amoA) ammonia-oxidizing bacteria (AOB). This indicated that conversion NH4+-N decreased nitrification process increased. brief, "source" "sink" NH4+-N, thus reducing retention alkaline soil, volatilization. These results is control strategy agricultural emission, maintaining high crop yield environmental disturbance.

Language: Английский

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Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters

Environmental Microbiology, Journal Year: 2014, Volume and Issue: 17(8), P. 2677 - 2689

Published: July 11, 2014

Network and multivariate statistical analyses were performed to determine interactions between bacterial fungal community terminal restriction length polymorphisms as well soil properties in paired woodland pasture sites. Canonical correspondence analysis (CCA) revealed that shifts composition correlated with dissolved organic carbon, while changes moisture, nitrogen phosphorus. Weighted correlation network detected two distinct microbial modules per land use. Bacterial ribotypes did not group separately, rather all comprised of both ribotypes. Woodland had a similar : ribotype ratio, the pasture, one module was dominated. There no their composition. The different relationships variables, these contrasts without use analysis. This study demonstrated fungi bacteria, components communities usually treated separate functional groups CCA approach, co-correlated formed associations adjacent habitats. Understanding modular may shed more light on niche space environment, allow realistic description ecology function.

Language: Английский

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Ammonium sorption and ammonia inhibition of nitrite-oxidizing bacteria explain contrasting soil N2O production

Scientific Reports, Journal Year: 2015, Volume and Issue: 5(1)

Published: July 16, 2015

Abstract Better understanding of process controls over nitrous oxide (N 2 O) production in urine-impacted ‘hot spots’ and fertilizer bands is needed to improve mitigation strategies emission models. Following amendment with bovine ( Bos taurus ) urine (Bu) or urea (Ur), we measured inorganic N, pH, N O genes associated nitrification two soils (‘ L ’ ‘ W ’) having similar texture, C C/N ratio. Solution-phase ammonia sl NH 3 was also calculated accounting for non-linear ammonium (NH 4 + sorption capacities (ASC). Soil displayed greater rates nitrate (NO − levels than soil , but more resistant nitrite accumulation produced ten times less . Genes NO oxidation nxr A) increased substantially remained static strongly correlated cumulative c- explained 87% the variance Differences between were by which inhibited oxidization leading production. This first study correlate dynamics nitrifier show how ASC can regulate

Language: Английский

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Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil

The ISME Journal, Journal Year: 2014, Volume and Issue: 8(12), P. 2397 - 2410

Published: May 23, 2014

Language: Английский

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Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere

Systematic and Applied Microbiology, Journal Year: 2018, Volume and Issue: 42(2), P. 248 - 260

Published: Nov. 6, 2018

Language: Английский

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