Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

Mukhtar, Hussnain; Lin, Yu‐Pin; Anthony, Johnathen

doi:10.3390/environments4040084

Cited by 14 publications

(8 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…AOA was represented several folds higher than AOB in all the cultivation stages (Figure 4C). In line to our observation, meta-analysis of East Asian paddy soils have found similar dominance of AOA over AOB in acidic as well as alkaline paddy soils (Mukhtar et al, 2017). AOA have been shown to be highly adaptive in microaerophilic condition (Wang et al, 2015) and greatly influence by the rice root exudates (Chen et al, 2008).…”

Section: Discussionsupporting

confidence: 90%

“…As for AOB community, Nitrosospira was the most dominant. Similar observation were found in alkaline as well as neutral paddy soil from China (Chen et al, 2008; Lu et al, 2018), Japan (Bowatte et al, 2006), East Asian paddy soils meta-analysis (Mukhtar et al, 2017). AOA has been found to be dominating in acidic soils (pH < 5.5) (Liu et al, 2013).…”

Section: Discussionsupporting

confidence: 80%

“…Nitrosophaera cluster was the 2nd most dominant group in our study. However, Nitrosophaera cluster was the most dominated within AOA community in several studies from China (Chen et al, 2008; Ke et al, 2013; Wang et al, 2015; Lu et al, 2018) and East Asian paddy soils meta-analysis (Mukhtar et al, 2017). The disparity between our study and literature could be attributed to the major difference in PCR primer.…”

Section: Discussionmentioning

confidence: 97%

See 2 more Smart Citations

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

et al. 2019

View full text Add to dashboard Cite

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

show abstract

Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 97%

See 1 more Smart Citation

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Nitrification is the most crucial step in the biogeochemical nitrogen (N) cycle in which NH 3 is oxidized to NO 2 − and then to NO 3 − [ 1 , 2 , 3 ]. The nitrification process regulates the absorption and availability of N to crops in the soil ecosystem [ 4 , 5 ] and may also cause the loss of N because leaching of NO 3 − is much easier than NH 3 [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization

Xie

et al. 2022

IJERPH

View full text Add to dashboard Cite

Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha−1 yr−1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha−1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g−1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g−1 dry soil with the N105 treatment (105 kg N ha−1 yr−1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha−1 yr−1 was optimum for the AOB community and wheat yield in the semi-arid area.

show abstract

“…Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) majorly dominate ecosystem functioning by modulating the rate of nitrification in terrestrial and aquatic ecosystems [1][2][3][4]. Ammonia oxidation is also carried out by complete ammonia oxidizers (comammox) [5,6].…”

Section: Introductionmentioning

confidence: 99%

Measuring Responses of Dicyandiamide-, 3,4-Dimethylpyrazole Phosphate-, and Allylthiourea-Induced Nitrification Inhibition to Soil Abiotic and Biotic Factors

Lin

Ansari

Cheng

et al. 2021

IJERPH

Self Cite

View full text Add to dashboard Cite

Nitrification inhibitors (NIs) such as dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and allylthiourea (AT) are commonly used to suppress ammonia oxidization at different time scales varying from a few hours to several months. Although the responses of NIs to edaphic and temperature conditions have been studied, the influence of the aforementioned factors on their inhibitory effect remains unknown. In this study, laboratory-scale experiments were conducted to assess the short-term (24 h) influence of eight abiotic and biotic factors on the inhibitory effects of DCD, DMPP, and AT across six cropped and non-cropped soils at two temperature conditions with three covariates of soil texture. Simultaneously, the dominant contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to potential ammonia oxidization (PAO) were distinguished using the specific inhibitor 2 phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). Our results revealed that AT demonstrated a considerably greater inhibitory effect (up to 94.9% for an application rate of 75 mg of NI/kg of dry soil) than DCD and DMPP. The inhibitory effect of AT was considerably affected by the relative proportions of silt, sand, and clay in the soil and total PAO. In contrast to previous studies, the inhibitory effects of all three NIs remained largely unaffected by the landcover type and temperature conditions for the incubation period of 24 h. Furthermore, the efficacy of all three tested NIs was not affected by the differential contributions of AOA and AOB to PAO. Collectively, our results suggested a limited influence of temperature on the inhibitory effects of all three NIs but a moderate dependence of AT on the soil texture and PAO. Our findings can enhance the estimation of the inhibitory effect in soil, and pure cultures targeting the AOA and AOB supported ammonia oxidization and, hence, nitrogen dynamics under NI applications.

show abstract

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

Cited by 14 publications

References 37 publications

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization

Measuring Responses of Dicyandiamide-, 3,4-Dimethylpyrazole Phosphate-, and Allylthiourea-Induced Nitrification Inhibition to Soil Abiotic and Biotic Factors

Contact Info

Product

Resources

About