Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

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Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

Applied and Environmental Microbiology ◽

10.1128/aem.05787-11 ◽

2011 ◽

Vol 77 (24) ◽

pp. 8635-8647 ◽

Cited By ~ 154

Author(s):

Man-Young Jung ◽

Soo-Je Park ◽

Deullae Min ◽

Jin-Seog Kim ◽

W. Irene C. Rijpstra ◽

...

Keyword(s):

16S Rrna ◽

Agricultural Soil ◽

Ammonia Oxidizing Bacteria ◽

Sequence Comparisons ◽

Soil Nitrification ◽

Content Type ◽

Group I ◽

Single Sequence

ABSTRACTSoil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizingArchaeafrom soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescencein situhybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaealamoAgenes featured a single sequence each. No bacterialamoAgenes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of13C intoArchaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “CandidatusNitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2%amoAgene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “CandidatusNitrosoarchaeum koreensis.”

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The effect of nitrogen fertilizers on irrigated cotton at the Kimberley Research Station, north-western Australia

Australian Journal of Experimental Agriculture ◽

10.1071/ea9650218 ◽

1965 ◽

Vol 5 (18) ◽

pp. 218 ◽

Cited By ~ 1

Author(s):

NJ Thomson

Keyword(s):

Plant Size ◽

Nitrogen Fertilizers ◽

Research Station ◽

Nitrogen Application ◽

High Nitrogen ◽

Lint Percentage ◽

Soil Nitrification ◽

Varied Response ◽

North Western ◽

Very High

Three experiments were carried out at Kimberley Research Station, W.A., between 1959 and 1963 to study the effects of rates and times of applying nitrogen fertilizer to irrigated cotton. Nitrogen applications increased yields in all three experiments but the magnitude of response varied. Response to nitrogen was greater after a short dry season fallow between crops than after a long fallow with accompanying soil nitrification. Very high nitrogen applications produced rank plant growth. The rank growth resulted in inefficient mechanical harvesting and the control of Prodenia litura was made difficult. Plant size was reduced by splitting the nitrogen application but yield was not reduced. Nitrogen applications had no effect on quality but reduced lint percentage slightly.

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Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

BioMed Research International ◽

10.1155/2015/582938 ◽

2015 ◽

Vol 2015 ◽

pp. 1-12 ◽

Cited By ~ 6

Author(s):

Mariusz Cycoń ◽

Zofia Piotrowska-Seget

Keyword(s):

Community Structure ◽

Denaturing Gradient Gel Electrophoresis ◽

Wiener Index ◽

Nitrification Rate ◽

Ammonia Oxidizing Bacteria ◽

Community Members ◽

Insecticide Treatment ◽

Soil Nitrification ◽

Ammonia Oxidizing Archaea ◽

Gradient Gel Electrophoresis

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the10*FRdosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of theSandHvalues in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of theSandHvalues was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

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Combined proteomics, metabolomics and physiological analyses of rice growth and grain yield with heavy nitrogen application before and after drought

BMC Plant Biology ◽

10.1186/s12870-020-02772-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Jie Du ◽

Tianhua Shen ◽

Qiangqiang Xiong ◽

Changlan Zhu ◽

Xiaosong Peng ◽

...

Keyword(s):

Drought Stress ◽

Drought Resistance ◽

Rice Variety ◽

Soluble Sugar ◽

Enrichment Analysis ◽

Nitrogen Management ◽

Nitrogen Regulation ◽

Growth And Yield ◽

Nitrogen Application ◽

Heavy Nitrogen

Abstract Background Nitrogen application can effectively mitigate the damage to crop growth and yield caused by drought. However, the efficiency of heavy nitrogen application before drought (NBD) and heavy nitrogen application after drought (NAD) to regulate rice response to drought stress remains controversial. In this study, we profiled physiology, proteomics and metabolomics in rice variety Wufengyou 286 of two nitrogen management modes (NBD and NAD) to investigate their yield formation and the mechanism of nitrogen regulation for drought resistance. Results Results revealed that the yield of NBD and NAD decreased significantly when it was subjected to drought stress at the stage of young panicle differentiation, while the yield of NBD was 33.85 and 36.33% higher than that of NAD in 2017 and 2018, reaching significant levels. Under drought conditions, NBD increased chlorophyll content and net photosynthetic rate in leaves, significantly improved the activities of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase and catalase, and decreased malondialdehyde (MDA) content compared with NAD. NBD promoted nitrogen assimilation in leaves, which was characterized by increased activities of nitrate reductase (NR) and glutamine synthetase (GS). In addition, NBD significantly increased the contents of osmotic regulatory substances such as soluble sugar, soluble protein and free proline. Gene ontology and KEGG enrichment analysis of 234 differentially expressed proteins and 518 differential metabolites showed that different nitrogen management induced strong changes in photosynthesis pathway, energy metabolism pathway, nitrogen metabolism and oxidation-reduction pathways. Conclusion Different nitrogen management methods have significant differences in drought resistance of rice. These results suggest that heavy nitrogen application before drought may be an important pathway to improve the yield and stress resistance of rice, and provide a new ecological perspective on nitrogen regulation in rice.

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Community Structure of Ammonia-Oxidizing Bacteria under Long-Term Application of Mineral Fertilizer and Organic Manure in a Sandy Loam Soil

Applied and Environmental Microbiology ◽

10.1128/aem.01536-06 ◽

2006 ◽

Vol 73 (2) ◽

pp. 485-491 ◽

Cited By ~ 160

Author(s):

Haiyan Chu ◽

Takeshi Fujii ◽

Sho Morimoto ◽

Xiangui Lin ◽

Kazuyuki Yagi ◽

...

Keyword(s):

Community Structure ◽

Mineral Fertilizer ◽

N Fertilization ◽

Organic Manure ◽

N Fertilizer ◽

Ammonia Oxidizing Bacteria ◽

Fertilizer N ◽

Soil Nitrification ◽

Nitrification Potential

ABSTRACT The effects of mineral fertilizer (NPK) and organic manure on the community structure of soil ammonia-oxidizing bacteria (AOB) was investigated in a long-term (16-year) fertilizer experiment. The experiment included seven treatments: organic manure, half organic manure N plus half fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). N fertilization greatly increased soil nitrification potential, and mineral N fertilizer had a greater impact than organic manure, while N deficiency treatment (PK) had no significant effect. AOB community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the amoA gene, which encodes the α subunit of ammonia monooxygenase. DGGE profiles showed that the AOB community was more diverse in N-fertilized treatments than in the PK-fertilized treatment or the control, while one dominant band observed in the control could not be detected in any of the fertilized treatments. Phylogenetic analysis showed that the DGGE bands derived from N-fertilized treatments belonged to Nitrosospira cluster 3, indicating that N fertilization resulted in the dominance of Nitrosospira cluster 3 in soil. These results demonstrate that long-term application of N fertilizers could result in increased soil nitrification potential and the AOB community shifts in soil. Our results also showed the different effects of mineral fertilizer N versus organic manure N; the effects of P and K on the soil AOB community; and the importance of balanced fertilization with N, P, and K in promoting nitrification functions in arable soils.

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High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils

Applied Soil Ecology ◽

10.1016/j.apsoil.2014.09.003 ◽

2015 ◽

Vol 85 ◽

pp. 21-29 ◽

Cited By ~ 36

Author(s):

Jing Che ◽

Xue Qiang Zhao ◽

Xue Zhou ◽

Zhong Jun Jia ◽

Ren Fang Shen

Keyword(s):

Ammonia Oxidizing Bacteria ◽

Acidic Soils ◽

Soil Nitrification ◽

High Ph

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Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

Applied and Environmental Microbiology ◽

10.1128/aem.00426-15 ◽

2015 ◽

Vol 81 (9) ◽

pp. 3218-3227 ◽

Cited By ~ 22

Author(s):

Jun Zhao ◽

Baozhan Wang ◽

Zhongjun Jia

Keyword(s):

High Throughput ◽

Paddy Soil ◽

Stable Isotope Probing ◽

Paddy Fields ◽

16S Rrna Genes ◽

Rrna Genes ◽

Molecular Evidence ◽

Ammonia Oxidizing Bacteria ◽

Soil Nitrification ◽

Content Type

ABSTRACTPaddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaealamoAgene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance ofNitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), andNitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of13C-labeled DNA further revealed that13CO2was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA andNitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated withNitrosospirasp. strain L115 and theNitrosospira multiformislineage and that the13C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic “CandidatusNitrososphaera gargensis,” uncultured fosmid 29i4, and acidophilic “CandidatusNitrosotalea devanaterra” lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields.

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