Leaf leachates have the potential to influence soil nitrification via changes in ammonia‐oxidizing archaea and bacteria populations

2019 ◽  
Author(s):  
W. B. Chen ◽  
B. M. Chen ◽  
H. X. Liao ◽  
J. Q. Su ◽  
S. L. Peng
Keyword(s):  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

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.

scholarly journals Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Ammonia Oxidation ◽  
Chemical Properties ◽  
Paddy Soils ◽  
Soil Nitrification ◽  
Treated Soil ◽  
Ammonia Oxidizing Archaea ◽  
Rice Yields ◽  
Traditional Irrigation ◽  
Almost All ◽  
And Function

AbstractBecause ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO 2 -  –N g-1 d.w.day-1) was found in T2 (optimal irrigation and fertilization)—treated soils, whereas the lowest PAO (0.004 μg NO 2 -  –N g-1 d.w.day-1) in T0 (traditional irrigation)- treated soils. Compared with the T0—treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2—treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2—treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.

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

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
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.

scholarly journals Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature

2019 ◽  
Vol 7 (11) ◽  
pp. 526 ◽  
Author(s):  
Hussnain Mukhtar ◽  
Yu-Pin Lin ◽  
Chiao-Ming Lin ◽  
Yann-Rong Lin
Keyword(s):  
Temperature Gradient ◽  
Relative Abundance ◽  
Temperature Response ◽  
Rate Theory ◽  
Fixed Temperature ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea ◽  
Different Temperatures ◽  
Order Of Magnitude ◽  
The Impact

Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity ( Δ C P ‡ ) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.

Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization

2021 ◽  
Vol 21 (4) ◽  
pp. 1800-1814
Author(s):  
Feng Wang ◽  
Xiaolong Liang ◽  
Shihan Ma ◽  
Lingzhi Liu ◽  
Jingkuan Wang
Keyword(s):  
Nitrogen Fertilization ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea

scholarly journals Archaea Are the Major Responsive Ammonia Oxidizers in a Paddy Soil Following Fertilization and Irrigation

2020 ◽  
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Community Composition ◽  
Ammonia Oxidation ◽  
Chemical Properties ◽  
Paddy Soils ◽  
Environmental Drivers ◽  
Soil Nitrification ◽  
Treated Soil ◽  
Ammonia Oxidizing Archaea ◽  
Traditional Irrigation ◽  
Almost All

Abstract Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their specific environmental drivers in paddy soils under different fertilization and irrigation regimes remains unclear. In this study, we investigated archaeal abundance, activity and community composition in acid paddy soils by a 10-year field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 µg NO2−-N g− 1 d.w.day− 1) was found in T2 (optimal irrigation and fertilization) - treated soils, whereas the lowest PAO (0.004 µg NO2−-N g− 1 d.w.day− 1) in T0 (traditional irrigation)- treated soils. Compared with the T0 - treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2 - treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The archaeal phylum Crenarchaeota and genus Candidatus Nitrosotalea were mainly found in the T2-treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Together, our findings confirmed that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain optimum rice yields in a subtropical paddy field.

scholarly journals Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

2012 ◽  
Vol 6 (11) ◽  
pp. 2024-2032 ◽  
Author(s):  
Anne E Taylor ◽  
Lydia H Zeglin ◽  
Thomas A Wanzek ◽  
David D Myrold ◽  
Peter J Bottomley
Keyword(s):  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea

Ammonia-Oxidizing Archaea Play a Predominant Role in Acid Soil Nitrification

2014 ◽  
pp. 261-302 ◽  
Author(s):  
Hang-Wei Hu ◽  
Zhi-Hong Xu ◽  
Ji-Zheng He
Keyword(s):  
Acid Soil ◽  
Predominant Role ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea

scholarly journals (S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Liu ◽  
Daniel M. Schubert ◽  
Martin Könneke ◽  
Ivan A. Berg
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Fusion Protein ◽  
Inorganic Carbon ◽  
Primary Control ◽  
Acetyl Coa ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea ◽  
Highly Active ◽  
Dehydrogenase Reaction

Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Here, we heterologously produced the protein Nmar_1028 catalyzing this reaction in thaumarchaeon Nitrosopumilus maritimus, characterized it biochemically and performed its phylogenetic analysis. This NAD-dependent dehydrogenase is highly active with its substrate, (S)-3-hydroxybutyryl-CoA, and its low Km value suggests that the protein is adapted to the functioning in the 3-hydroxypropionate/4-hydroxybutyrate cycle. Nmar_1028 is homologous to the dehydrogenase domain of crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase that is present in many Archaea. Apparently, the loss of the dehydratase domain of the fusion protein in the course of evolution was accompanied by lateral gene transfer of 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase from Bacteria. Although (S)-3-hydroxybutyryl-CoA dehydrogenase studied here is neither unique nor characteristic for the HP/HB cycle, Nmar_1028 appears to be the only (S)-3-hydroxybutyryl-CoA dehydrogenase in N. maritimus and is thus essential for the functioning of the 3-hydroxypropionate/4-hydroxybutyrate cycle and for the biology of this important marine archaeon.

scholarly journals Effects of Salt on Root Aeration, Nitrification, and Nitrogen Uptake in Mangroves

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1131 ◽  
Author(s):  
Yan Zhao ◽  
Xun Wang ◽  
Youshao Wang ◽  
Zhaoyu Jiang ◽  
Xiaoyu Ma ◽  
...  
Keyword(s):  
N Uptake ◽  
Avicennia Marina ◽  
Root Anatomy ◽  
Root Porosity ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea ◽  
Gene Copies ◽  
Negative Effect ◽  
Moderate Salinity ◽  
Root Aeration

The potential effects of salt on the growth, root anatomy, radial oxygen loss (ROL), and nitrogen (N) dynamics in mangroves were investigated using the seedlings of Avicennia marina (Forsk.) Vierh. The results showed that a moderate salinity (200 mM NaCl) appeared to have little negative effect on the growth of A. marina. However, higher salt stresses (400 and 600 mM NaCl) significantly inhibited the biomass yield. Concentrations of N in the roots and leaves decreased sharply with increasing salinity. Nevertheless, the presence of salt directly altered root anatomy (e.g., reduced root porosity and promoted suberization within the exodermis and endodermis), leading to a significant reduction in ROL. The results further showed that reduced ROL induced by salt could restrain soil nitrification, resulting in less ammonia-oxidizing archaea and bacteria (AOA and AOB) gene copies and lower concentrations of NO3− in the soils. While increased root suberization induced by salt inhibited NH4+ and NO3− uptake and influx into the roots. In summary, this study indicated that inhibited root aeration may be a defense response to salt, however these root symptoms were not advantageous for rhizosphere nitrification and N uptake by A. marina.

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