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Effect of soil acidification on nitrification in soil
Canadian Journal of Soil Science
Abstract
Zebarth, B. J., Forge, T. A., Goyer, C. and Brin, L. D. 2015. Effect of soil acidification on nitrification in soil. Can. J. Soil Sci. 95: 359–363. This laboratory experiment examined the effect of elemental S-induced variation in soil pH (3.97–5.29) on nitrification enzyme activity and conversion of [Formula: see text] to [Formula: see text]. Nitrification rate generally decreased with decreasing soil pH, but still proceeded rapidly within the pH range (4.5 to 5.2) recommended for blueberry production, contrary to what is generally assumed.
... Soil pH is a crucial factor for the nitrification process, and it occurs in a wide range of soil pH [29,30], although the pH range from 6.5 to 8.5 is considered optimal [29]. Zebarth et al. [31] conducted a laboratory experiment to investigate nitrification under acidic conditions. The authors reported that the process of nitrification occurred in an acidic pH range from 3.97 to 5.29, but the activity of the nitrification enzyme was higher in the pH range of 4.5-5.2 ...
... The authors reported that the process of nitrification occurred in an acidic pH range from 3.97 to 5.29, but the activity of the nitrification enzyme was higher in the pH range of 4.5-5.2 [31]. In another four-year field experiment carried out by Kyverga et al. [32] in maize (Zea mays L.) soil, the authors found that 89% of total nitrification occurred in the soil with a pH less than 7.5. ...
Nitrous oxide (N2O) is a potent greenhouse gas, and agriculture represents more than fifty percent of total anthropogenic emissions. The production of N2O in soil is biogenic through nitrification, denitrification, chemonitrification, nitrifier denitrification, etc., which are processes influenced by the soil pH, temperature, moisture, oxygen concentration, organic carbon, and soil nitrogen. Higher N2O emissions from the soil result in lower nitrogen use efficiency and higher environmental pollution in terms of global warming. Therefore, an understanding of different pathways for N2O production in soil and the affecting factors is essential to mitigate N2O emissions from soil to the atmosphere. Nitrification inhibitor application has been reported in many studies, but the impact of nitrification inhibitors in different perennials (orchards) and biennials (rice, wheat, maize, etc.) is not lacking. In this study, we develop an understanding of different N2O production pathways and different influencing factors. The role of the different nitrification inhibitors was also developed to achieve low N2O emissions from soils to the atmosphere.
... The recommended pH water range to grow cranberry is broadly defined as between 4.0 and 5.5 [2]. Nitrification is inhibited at pH water ≤ 4.2, curbing the growth of nitrophilous weeds [3]. Ammonium sulfate contributes to soil acidification following ammonium transformation into nitrate [4]. ...
... Temperature regulates the biological transformations of ammonium and elemental sulfur [3]. Elemental S mitigates pest propagation and the severity of fungal diseases through pH change [11]. ...
... Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are the key microorganisms, which can regulate the transport and existence of nitrogen in the soil, thus affecting the efficient use of nitrogen fertilizer [21]. Ammonia-oxidizing microorganisms respond to many environmental factors [22], such as pH [23], temperature [24], NH3 molecular concentration [25] and moisture [26,27]. Among them, moisture is an important factor to its growth [28]. ...
... Among them, ammonia-oxidizing bacteria (AOB) and ammoniaoxidizing archaea (AOA) are the key microorganisms, which can regulate the transport and existence of nitrogen in the soil, thus affecting the efficient use of nitrogen fertilizer [21]. Ammonia-oxidizing microorganisms respond to many environmental factors [22], such as pH [23], temperature [24], NH 3 molecular concentration [25] and moisture [26,27]. Among them, moisture is an important factor to its growth [28]. ...
Water ionization is an efficient physical water treatment technology, and crop water and nutrient use efficiencies can be improved using ionized water for irrigation. In order to explore the effect of ionized water on soil nitrification and nitrifying microorganisms, we conducted a laboratory soil incubation experiment with the addition of ionized water and ordinary water under different soil water contents (equal to 30%, 60%, 100% and 175% of the field capacity, θFC). During the soil incubation, we analyzed soil inorganic nitrogen transformation, ammonia oxidation gene abundances and nitrifying microbial community structure. The results showed that, no matter adding ordinary water or ionized water, the soil nitrification rate and the abundance of ammonia oxidizing bacteria in the 100%θFC treatment were significantly higher than those in other water conditions, while the abundance of ammonia oxidizing archaea was not affected by the soil water content. With the same soil water content, the nitrification rate of ionized water treatment was stronger than that of the ordinary water treatment. Although the absolute abundance of ammonia-oxidizing microorganisms in ionized water treatment was significantly lower than that of ordinary water (p < 0.05), the relative abundance of some dominant nitrifying microbial genera in the ionized water treatment was significantly higher (p < 0.05). The dominant genera may play a key role in the nitrification process. The results show that ionized water irrigation can significantly promote the nitrification of silt loam soil, especially under 100%θFC conditions, and may regulate soil nitrification by affecting some dominant nitrifying microorganisms. This study provides a theoretical basis for understanding the biological regulation mechanism of ionized water irrigation on soil nutrient transformation and for application of ionized water to field irrigation.
... The soil column simulation test constitutes a widely utilized methodology for the investigation of soil acidification processes [30,31]. A soil column acidification culture test was conducted on soil collected in September 2018 from the southeast of Jilin Agricultural University (125°25.025′E, ...
The excessive utilization of chemical fertilizers, particularly nitrogen fertilizers, is leading to decline in the pH level of the black soil in Jilin Province. Acidification of black soil leads to reduced salt base saturation, decreased organic matter content, and increased soil degradation, which, in turn, leads to diminshed aggregate stability and poor soil structure, negatively affecting soil fertility. As a result, the sustainability of food production and farmland ecosystem stability are at risk. The precise relationship between alterations in cementing substances and changes in soil aggregate stability during the acidification of black soil remains unclear, and the ultrasonic thermal difference method allows for the quantitative description of changes in soil aggregate stability. Therefore, this study employed the ultrasonic thermal difference method to investigate the impact of acidification on the stability of black soil aggregates and their cementing substances through a simulated fertilizer drenching experiment, thus elucidate the relationship between primary cementing materials and the stability of aggregates under varying degrees of black soil acidification, and to provides theoretical basis and data for alleviating and preventing acidification of black soil in Jilin Province. The results disclosed a gradual decline in soil organic carbon (SOC) levels during the acidification experiment, while water-soluble organic carbon (WSOC) first increased and then decreased. After 25 years of simulated leaching, SOC decreased by 1.34% and WSOC declined by 15.63%. Acidification has a minimal impact on Fe-Al bonded organic carbon but significantly reduces calcium-bonded organic carbon by 17.07% over 25 years. The content of exchangeable Ca²⁺ and Mg²⁺ decreases as acidification intensifies. After 25 years, exchangeable Ca²⁺ and Mg²⁺ decreased by 9.42% and 7.00%, respectively. The acidification of the test soil resulted in a 46.5% reduction in the aggregate stability energy (E) of water-stable microaggregates, with an average decrease of 14.04 J/g for every 0.1 unit decrease in pH. Additionally, the soil critical stabilization energy (Ecrit) exhibited a 51.48% reduction. The results demonstrated that a decrease of 0.32 J/g in E was associated with a 0.1 unit decrease in pH on average. Furthermore, the multivariate linear regression analysis revealed that the reduction in soil organic carbon (SOC) content contributed the most to the decline in E, followed by Calcium bond-bound soil organic carbon (Ca-SOC). Notably, Ca-SOC exerted the greatest influence on the reduction in sand grain Ecrit, followed by SOC.
... High pH favours formation of ammonia (NH 3 ) from NH 4 + , which may volatilise, while the non-volatised NH 4 + can be oxidised into NO 3 − via nitrification. This causes soil acidification (Subbarao et al. 2006) and because of acidification, the rate of nitrification will also be reduced (Hanan et al. 2016;Zebarth et al. 2015). ...
Purpose
Inconsistent yield responses to inorganic phosphorus (P) fertilisers in tropical rice paddy soils remain a challenge. This study investigated the contributions of applied P fertilisers to soluble soil P and P transformation mechanisms in P-added paddy soils.
Methods
An incubation study was conducted on three rice-growing soils (Ultisol, Alfisol, and Entisol) in Sri Lanka with and without single superphosphate (SSP), triple superphosphate (TSP), and urea. Dissolved reactive phosphorus (DRP) was measured over 112 days of submergence. Thermodynamic modelling and chemical P fractionation were employed to assess soil P transformations.
Results
Phosphorus-fertilised soils had significantly higher DRP concentrations (1.1–8.0 mg L ⁻¹ ) compared to controls at 7 days after submergence but DRP declined beyond 21 days (0.024–0.300 mg L ⁻¹ ). Single superphosphate increased DRP more than TSP, short-term. Urea did not affect DRP concentration. Ultisols exhibited the lowest DRP, while Alfisols maintained higher DRP than Ultisol which was near or above the critical concentration for rice (0.1 mg L⁻ ¹ ) after 28 days. In Entisol, only SSP maintained DRP above 0.1 mg L ⁻¹ . Modelling suggested Ca phosphates and Fe oxy(hydr)oxides dissolved during submergence. Released P may be resorbed by Fe/Al oxy(hydr)oxides and Ca minerals, with evidence of downward movement of dissolved P and its resorption onto Fe/Al and Ca minerals possibly due to saturation of P sorption sites in the topsoil layer.
Conclusion
Low dissolved P in porewater may be linked to inherent soil characteristics, including low organic matter and high amorphous Fe and Al oxides.
... In more acidic soils, however, nitrification is inhibited, which reduces the availability of nitrate and forces plants to rely on ammonia as their primary nitrogen source. This shift can decrease nitrogen utilization efficiency (Zebarth et al., 2015). The results of this study show that the highest total nitrogen content is found in garden land use, with an average of 0.28%, and the highest individual value recorded at K2 (0.38%) (Figure 3). ...
This study was conducted in the Manten Sub-Watershed Catchment Area, Malang Regency, focusing on the districts of Bululawang, Tajinan, Wajak, and Poncokusumo. The research assessed three land use types-plantations, rice fields, and gardens-each represented by five sampling sites to capture the variation in land use across the region. Results revealed that garden soils exhibited superior chemical health compared to rice fields and plantations. Key soil limitations identified included low organic carbon content, cation exchange capacity (CEC), and base saturation (BS), all of which were found to restrict soil fertility in the study area. These findings highlight the urgent need for targeted soil management practices to enhance land productivity and promote sustainable agricultural practices in the region.
... Contrary to expectations, in Soil A, with higher levels of DMP than in Soil C, there was no inhibitor effect, as all treatments, including U, had N 2 O emissions similar to those of the control (Figure 2). This effect can be attributed to soil pH, as the nitrification rate is reduced in soils with acidic pH [43]. According to Li et al. [44], bacterial N 2 O reductase activity is inhibited under low pH conditions. ...
Studies of the impact of nitrification inhibitors (NIs), specifically DMPP and DMPSA, on N2O emissions during “hot moments” have produced conflicting results regarding their effectiveness after rewetting. This study aimed to clarify the effectiveness of NIs in reducing N2O emissions by assessing residual DMP concentration and its influence on ammonia-oxidizing bacteria (AOB) in two pot experiments using calcareous (Soil C, Calcic Haploxerept) and acidic soils (Soil A, Dystric Xerochrepts). Fertilizer treatments included urea (U), DMPP, and DMPSA. The experiments were divided into Phase I (water application to dry period, 44 days) and Phase II (rewetting from days 101 to 121). In both phases for Soil C, total N2O emissions were reduced by 88% and 90% for DMPP and DMPSA, respectively, compared with U alone. While in Phase I, the efficacy of NIs was linked to the regulation of AOB populations, in Phase II this group was not affected by NIs, suggesting that nitrification may not be the predominant process after rewetting. In Soil A, higher concentrations of DMP from DMPP were maintained compared to Soil C at the end of each phase. Despite this, NIs had no significant effect due to low nitrification rates and limited amoA gene abundance, indicating unfavorable conditions for nitrifiers. The study highlights the need to optimize NIs to reduce N2O emissions and improve nitrogen efficiency, while understanding their interactions with the soil. This knowledge is necessary in order to design fertilization strategies that improve the sustainability of agriculture under climate change.
... Second, that N 2 O-N was mainly produced via denitrification, and thus its 501 production decreased as increased microbial utilisation/immobilisation of nitrate N reduced soil Cumulative leached ammonium and nitrate varied between the Ferralsols and Nitisols likely 509 due to inherent differences in soil pH. This is because soil pH affects microbial transformation of 510 ammonium to nitrate (Zebarth et al., 2015) and thus the concentrations of these N forms in soil. 511 ...
... PCA and Pearson's correlation analyses revealed a mutual relation between 16S rDNA and the indicator of nitrification AOB (as well as dsr microbial indicators, Fig. 2C; 1A,B; 3D), supporting the hypothesis that changes in absolute bacterial abundance depend largely on shifts in the relative richness of distinct bacterial groups. The observed tendency towards S 0 -specific reduction in ammoniaoxidizing bacteria abundance (though significant only in the 0.5 S 0− NP + GO variant) and the indirect dependence of AOB on S 0 amendments to soil have been observed by other authors under conditions of very low pH [108]. While, in our work we observed that GO insignificantly affected AOB values (Fig. 2C), this contrasts with the reported adverse effect of GO on the abundance of ammonia oxidizers and nitrifiers [105,109]. ...
Background
Sulphur (S) deficiency has emerged in recent years in European soils due to the decreased occurrence of acid rains. Elemental sulphur (S⁰) is highly beneficial as a source of S in agriculture, but it must be oxidized to a plant-accessible form. Micro- or nano-formulated S⁰ may undergo accelerated transformation, as the oxidation rate of S⁰ indirectly depends on particle size. Graphene oxide (GO) is a 2D-carbon-based nanomaterial with benefits as soil amendment, which could modulate the processes of S⁰ oxidation. Micro-and nano-sized composites, comprised of S⁰ and GO, were tested as soil amendments in a pot experiment with unplanted soil to assess their effects on soil microbial biomass, activity, and transformation to sulphates. Fourteen different variants were tested, based on solely added GO, solely added micro- or nano-sized S⁰ (each in three different doses) and on a combination of all S⁰ doses with GO.
Results
Compared to unamended soil, nano-S⁰ and nano-S⁰+GO increased soil pH(CaCl2). Micro-S⁰ (at a dose 4 g kg⁻¹) increased soil pH(CaCl2), whereas micro-S⁰+GO (at a dose 4 g kg⁻¹) decreased soil pH(CaCl2). The total bacterial and ammonium oxidizer microbial abundance decreased due to micro-S⁰ and nano-S⁰ amendment, with an indirect dependence on the amended dose. This trend was alleviated by the co-application of GO. Urease activity showed a distinct response to micro-S⁰+GO (decreased value) and nano-S⁰+GO amendment (increased value). Arylsulfatase was enhanced by micro-S⁰+GO, while sulphur reducing bacteria (dsr) increased proliferation due to high micro-S⁰ and nano-S⁰, and co-amendment of both with GO. In comparison to nano-S⁰, the amendment of micro-S⁰+GO more increased soluble sulphur content more significantly.
Conclusions
Under the conditions of this soil experiment, graphene oxide exhibited a significant effect on the process of sulphur oxidation.
... Soil pH affects various soil biogeochemical processes, including organic matter decomposition, degradation of organic pollutants, rhizosphere dynamics, organic matter amendments, dissolution of organic matter and heavy metals, nitrification, denitrification, microbial indicators, soil enzyme activity, organic matter and heavy metal precipitation, ammonia release, and organic matter mineralization, among others (Neina, 2019). The rate of nitrification decreases when lower soil pH values are observed (Zebarth et al., 2015). C and N mineralizable components rise when the soil pH value increases. ...
The assessment of land’s agricultural potential, through a land capability evaluation, delves into its innate limitations, crop suitability, and responses to soil management. In regions where agriculture reigns supreme, socio-economic development is inexorably linked to the agricultural sector, making the optimal utilization of land resources an imperative pursuit. The pursuit of this objective is underpinned by the selection of new agricultural areas and the determination of which crops thrive in specific locations, for which the multi-criteria decision-making (MCDM) method emerges as an ideal choice. This comprehensive research endeavour revolves around the intricate interplay of climatic, edaphic, fertility, topographical, and socioeconomic determinants. Within this intricate web, a total of 15 determinants play a pivotal role, including precipitation, potential evapotranspiration (PET), soil texture, drainage, soil organic-carbon, nitrogen content, pH, clay content, river proximity, land use/land cover (LULC), slope, temperature, social suitability, irrigation density, and elevation. To weigh these determinants, the Analytical Hierarchy Process (AHP) comes into play, ultimately revealing that the dominant influences on land capability stem from the realms of climate and soil. The watershed’s terrain analysis revealed a distinct suitability contrast: 168 km² highly suitable, 181.3 km² moderate, and 429 km2 low. The eastern and northeastern sectors were notably promising. Rigorous validation, using the ROC curve, confirmed the reliability and precision. The process yielded an impressive 83.2% AUC, unequivocally confirming the assessment’s remarkable accuracy and dependability.
... Compared with the effect of MPs alone on NH þ 4 content that was not significant, MPs combined with acid rain significantly increased the NH þ 4 content (Figure 3b). This is because acid rain will reduce the soil pH value, and the decrease in pH will lead to the decrease in soil nitrification (Zebarth et al., 2015), thereby reducing the conversion of NH þ 4 to NO À 3 in the soil. Finally, our metaanalysis also found that compared with the effect of MPs alone on NH þ 4 content which was not significant, MPs combined with multi-walled carbon nanotubes significantly reduced NH þ 4 content (Figure 3b). ...
Microplastics (MPs) enter the global soil ecosystem in significant quantities, and in agricultural lands, interact with soil amendments (e.g, fertilisers, pesticides, biochar), pollutants (e.g., heavy metals and acid rain) and soil fauna (e.g., earthworms and microbial biomass) which impacts carbon (C) and nitrogen (N) cycling in soil in ways that are largely unexplored. Here, we analysed the difference in the responses of soil C and N contents, greenhouse gas emissions and soil enzyme activities in experiments where MPs alone or MPs in combination with other soil amendments or soil fauna had been explored, by conducting a global meta‐analysis of 2543 observational data extracted from 84 published studies. The results show that MPs alone are associated with significantly increased soil C storage and altered soil N pool composition, increased soil carbon dioxide (CO 2 ) and nitrous oxide (N 2 O) emissions, reduced soil ammonia (NH 3 ) emissions, increased activity of one of the five major enzymes related to C cycle, and increased activity of three of the four major enzymes related to N cycling in soil. Experiments that explored the combined effects of MPs combined with fertilisers on soil C and N contents and enzyme activities indicated greater effects than MPs alone. However, the effects of MPs combined with soil fauna, heavy metals, acid rain, glyphosate, and carbon nanotubes on soil C and N cycling differed from findings of studies that considered the effects of MPs alone. The results of this meta‐analysis provide a theoretical basis for further study of the effects of MPs on C and N cycling in fertilized agricultural soil, compound‐contaminated soil and acidified soil. We also show that, despite the global importance of MPs in soil, the number of studies of their effects on soil C and N cycling is relatively few, and further research on the mechanisms of interactions of MPs with multiple soil amendments in soil systems is urgently needed.
... However, it is in contrast with the field trial carried out by Seidel et al. (2017) where no effect was observed. Due to the similarity in the nitrification patterns for both slurry treatments, in addition to the absence of the direct effect of pH reduction on nitrification rate (Zebarth et al., 2015), we presume that the enhanced nitrification in the acidified slurry treatment is mostly attributed to the higher content of NH 4 + available for nitrification (Fangueiro et al., 2015;Frampton et al., 1999;Zaman et al., 1999). Thus, the consistent increase in extractable soil NO 3 − concentrations in soil pore water for all treatments indicates continuous mineralization of soil organic matter to NH 4 + and almost immediate nitrification (Jones et al., 2004). ...
... Considering that nitrification is pH-sensitive and that the rate declines at low pH values (Ste-Marie and Paré 1999, Zebarth et al. 2015), the soil pH was screened before and after the experiment using a handheld pH meter (Hach-H-Series H160, Loveland, CO, USA) equipped with an ISFET sensor (Mettler Toledo, Stockholm, Sweden). ...
Amidst population growth, escalating food costs, limited arable land, and farmland degradation, the adoption of innovative technologies—like organic waste recycling and nutrient recovery—is crucial for enhancing the resilience of global agri-food systems. Nitrogen-Enriched Organic fertilizer (NEO) is produced using a new method, where dinitrogen (N2) is captured from the air through a plasma process and mixed with slurries or digestates as nitrate (NO3-) and nitrite (NO2-). This process leads to solid slurry acidification and a high NO2- content, potentially yielding toxic inorganic or organic N compounds. This study investigated the impact of NEO derived from cattle slurry and biogas digestate on soil nitrification—conversion of NH4+ to NO2- and NO3- by aerobic autotrophic bacteria and archaea. We investigated and compared the potential nitrification rates in soil samples from two agricultural trials (cereal and grass) treated with NEO and other fertilizers after two consecutive fertilization years. Additionally, we examined the immediate nitrification response to NEO through 73-hour soil incubations. Our results revealed that NEO significantly stimulated nitrification rates in agitated soil slurries, regardless of the feedstock used, surpassing rates observed in ammonium controls. Similarly, this pattern was also observed in loosely placed soil samples, with high nitrification rates occurring with NEO and ammonium chloride. Interestingly, the differences in nitrification rates between field-fertilized soil samples were minimal and inconsequential, suggesting that while NEO exhibits a rapid boost in nitrification rates shortly after application, this effect is not sustained ≈ six months after fertilization under field conditions. Consequently, NEO indicates its potential as an environmentally benign fertilizer without adversely affecting soil nitrification.
Keywords: environment, innovative fertilizers, nitrogen, manure, sustainability, resilience, waste management
... Soil microbial populations and their relative activities in biogeochemical processes are affected by changes in soil pH (Bernhard et al., 2010). Among soil microbial communities, especially ammonia oxidizers, changes in soil pH greatly influence bacterial growth and activities (Zebarth et al., 2015), and depict the relative abundance of soil ammonia oxidizers (Prosser and Nicol, 2012). Soil pH is one of the principal factors commanding the rates and end-product accumulations of nitrification (Kyveryga and Blackmer, 2018). ...
The abundance and structural composition of nitrogen (N) transformation-related
microbial communities under certain environmental conditions provide sufficient
information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4+-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various
soil factors, such as soil saturation, availability of NH4+, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
... La actividad microbiológica del suelo se presenta en un pH entre 5.5 a 8.8; fuera de estos rangos, la mineralización de la MO generalmente disminuye (Havlin 2020). Sin embargo, se han reportado procesos de nitrificación a pH 4.14 (Zebarth et al. 2015), lo cual indica posibles aportes de N en suelos fuertemente ácidos, como se presentó en los huertos 8 y 13. ...
... Therefore, we expect that increases in shoot regrowth of grasses and sedges could partially be due to the release of resource competition in the presence of stressed forbs. Furthermore, an increase in EC as in- We found soil NH 4 + concentration increased but NO 3 − decreased with S addition (Figure 2c, acidification (Chen et al., 2013;Norton & Ouyang, 2019;Zebarth et al., 2015). However, shoot regrowth of grasses showed significant relationships with both soil NO 3 − and NH 4 + (Figure 4), which strongly suggest a great flexibility of grasses in taking up different N forms . ...
Soil acidification as a global change factor can devastatingly affect plant growth and productivity. In frequently disturbed ecosystems, plant resprouting ability strongly determines biomass reconstruction and resilience after above‐ground damage. However, how plant regrowth responds to soil acidification remains largely unknown for, especially regarding the role of rhizosphere in mediating this response.
We manipulated a soil‐acidification gradient via adding purified elemental sulphur powder at various rates (0–50 g S m⁻² year⁻¹) in a frequently mown meadow. Shoot regrowth of functional groups were measured after clipping and supporting roles of rhizosphere versus bulk soils were disentangled using isotope labelling along the acidification gradient.
Regrowth of grasses and sedges increased while forbs decreased along the acidification gradient. The results suggest that grasses were competitors capable of taking up nutrients from both rhizosphere and bulk soils, while sedges were acid‐tolerators with lower sensitivity to decreased nitrogen‐mineralization rates. Forbs, as typical ruderals, were vulnerable to N competition with microbes, particularly in the rhizosphere soil. Therefore, biomass regrowth of forbs was explained more by physicochemical and biological parameters from the rhizosphere than bulk soil.
Synthesis. Divergent interplay between plant functional groups and rhizosphere soils was the prominent driver for biomass regrowth responding to soil acidification.
... Soil microbial populations and their relative activities in biogeochemical processes are affected by changes in soil pH (Bernhard et al., 2010). Among soil microbial communities, especially ammonia oxidizers, changes in soil pH greatly influence bacterial growth and activities (Zebarth et al., 2015), and depict the relative abundance of soil ammonia oxidizers (Prosser and Nicol, 2012). Soil pH is one of the principal factors commanding the rates and end-product accumulations of nitrification (Kyveryga and Blackmer, 2018). ...
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4+-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4+, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
... Soil microbial populations and their relative activities in biogeochemical processes are affected by changes in soil pH (Bernhard et al., 2010). Among soil microbial communities, especially ammonia oxidizers, changes in soil pH greatly influence bacterial growth and activities (Zebarth et al., 2015), and depict the relative abundance of soil ammonia oxidizers (Prosser and Nicol, 2012). Soil pH is one of the principal factors commanding the rates and end-product accumulations of nitrification (Kyveryga and Blackmer, 2018). ...
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4⁺-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4⁺, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
... Bacteria represent an integral part of the microbial communities in soils, contributing greatly to the carbon (C) cycle and the availability of other nutrients (Lladó et al., 2017). By producing a wide range of enzymes and other extracellular polymeric substances, soil bacteria are metabolically versatile and actively participate in the catabolism of soil organic matter (SOM), nitrogen (N) and phosphorus (P) cycles, and other ecological processes (Datta et al., 2017;Gai et al., 2021;Zebarth et al., 2015). However, bacterial communities are sensitive to environmental change (Zeglin et al., 2011). ...
Soil oxygen (O2) deficiency induced by organic mulching is easy to overlook. Aeration has been shown to potentially alleviate soil hypoxia stress. However, the responses of soil bacterial communities to such mulching-induced hypoxic conditions and aeration remain elusive. Therefore, a three-year field experiment, consisting of mulching (T1), mulching with aeration (TA1, poor aeration; TA2, strong aeration), and no-mulching (CK) treatments, was conducted in bamboo (Phyllostachys praecox) plantations. According to our results, the strong aeration treatment (TA2) alleviated soil acidification, increased soil nutrient availability, and significantly increased soil O2 content by 18.44% (P < 0.05) when compared with T1. In addition, TA2 significantly increased soil β-glucosidase, invertase, urease, and acid phosphatase activities compared with CK and T1 (P < 0.05). The alpha diversity indices with TA2 treatment were the highest, indicating that aeration increased the species richness and diversity of bacteria. The changes in bacterial community composition associated with TA2 treatment (i.e., an increase in Firmicutes, Verrucomicrobia, and Faecalibacterium abundance and a decrease in Chloroflexi and Bradyrhizobium abundance) were mainly related to nutrient and O2 content. Mantel Test results suggested that soil O2 content and temperature were the key factors shaping bacterial community composition. Structural equation modeling revealed that soil O2 content had a positive and direct influence on bacterial community diversity. Functional annotation of prokaryotic taxa predicted that TA2 significantly increased the relative abundance of bacterial communities associated with nitrification, nitrogen fixation, and ureolysis. Our results demonstrated that optimal soil aeration conditions (17.60% of O2 content) could enhance the diversity and function of soil bacterial communities. Overall, the findings of this study could serve as a benchmark for alleviating soil hypoxia caused by organic mulches, which is important for increasing the functionality of nutrient cycling bacterial communities in the soil.
... Like CO 2 and CH 4 , N 2 O emission also showed a significantly strong correlation with pH. Other studies strongly supported our findings suggesting that ammonia-oxidizing and nitrifier communities might remain active at low soil pH contributing to soil N 2 O emission (Ariani et al., 2020;Zebarth et al., 2015). ...
Wetlands are emitters of greenhouse gases. However, many of the wetlands remain understudied (like temperate, boreal, and high-altitude wetlands), which constrains the global budgets. Himalayan foothill is one such data-deficient area. The present study reported (for the first time) the greenhouse gas fluxes (CO2, CH4, N2O, and H2O vapor) from the soils of the Nakraunda wetland of Uttarakhand in India during the post-monsoon season (October 2020 to January 2021). The sampling points covered six different types of soil within the wetlands. CO2, CH4, N2O, and H2O vapor emissions ranged from 82.89 to 1052.13 mg m⁻² h⁻¹, 0.56 to 2.25 mg m⁻² h⁻¹, 0.18 to 0.40 mg m⁻² h⁻¹, and 557.96 to 29,397.18 mg m⁻² h⁻¹, respectively, during the study period. Except for CO2, the other three greenhouse gas effluxes did not show any spatial variability. Soils close to “swamp proper” emitted substantially higher CO2 than the vegetated soils. Soil temperature exhibited exponential relationships with all the greenhouse gas fluxes, except for H2O vapor. The Q10 values for CO2, CH4, and N2O varied from 3.42 to 4.90, 1.66 to 2.20, and 1.20 to 1.30, respectively. Soil moisture showed positive relationships with all the greenhouse gas fluxes, except for N2O. The fluxes observed from Nakraunda were in parity with global observations. However, this study showed that wetlands experiencing lower temperature regime are also capable of emitting a substantial amount of greenhouse gases and thus, requires more study. Considering the seasonality of greenhouse gas fluxes should improve global wetland emission budgets.
... Yet, it was also reported that nitrification can occur rapidly within the pH range of 4.5-5.2 [18]. Both the amount and forms of SOM can also have substantial impacts upon N min , especially the labile C and N pools, given the positive correlation between the mineralization potential and SOM content [19]. ...
The mineralization of soil organic nitrogen (N) is the key process in the cycling of N in terrestrial ecosystems. Land-use change to bamboo (Phyllostachys praecox) cultivation that later entails organic material mulching combined with chemical fertilizer application will inevitably influence soil N mineralization (Nmin) and availability dynamics. However, the soil Nmin rates associated with various N fractions of P. praecox in response to land-use change and mulching are not well understood. The present study aimed to understand the effects of land-use change to P. praecox bamboo cultivation and organic material mulching on soil Nmin and availability. Soil properties and organic N fractions were measured in a P. praecox field planted on former paddy fields, a mulched P. praecox field, and a rice (Oryza sativa L.) field. Soil Nmin was determined using a batch incubation method, with mathematical models used to predict soil Nmin kinetics and potential. The conversion from a paddy field to P. praecox plantation decreased the soil pH, soil total N, and soil organic matter (SOM) content significantly (p < 0.05); the mulching method induced further soil acidification. The mulching treatment significantly augmented the SOM content by 7.08% compared with the no-mulching treatment (p < 0.05), but it decreased soil hydrolyzable N and increased the nonhydrolyzable N (NHN) content. Both the Nmin rate and cumulative mineralized N were lowest in the mulched bamboo field. The kinetics of Nmin was best described by the ‘two-pool model’ and ‘special model’. The Pearson’s correlation analysis and the Mantel test suggested soil pH was the dominant factor controlling the soil cumulative mineralized N and mineralization potential in the bamboo fields. These findings could help us better understand the N cycling and N availability under mulching conditions for shifts in land use, and provide a scientific basis for the sustainable management of bamboo plantations.
... Also of note was the decrease in NH 4 + -N capture for all treated soils compared with controls after week 3 (especially evident in soil 1), with NO 3 --N making up almost all N fluxes measured in weeks 6 and 10 ( Fig. 2 and Supplementary Fig. S2 1 ). This was likely related to the increase in soil pH noted for all treated soils (Table 3), which would tend to promote increased nitrification (Zebarth et al. 2015). ...
Two forest soil B-horizons were amended with alkaline-treated biosolids (ATB), powdered agricultural lime, and wood fly ash under controlled conditions to compare initial ion availabilities over a 10-week period. ATB was most effective in supplying available Ca²⁺ but least effective in supplying available Mg²⁺, for which lime was most effective. Availability of K⁺ and SO42–-S was greatest in fly ash amended soils because of high K and S loading rates and the high electrical conductivity of this amendment. Mineral N (NO3–-N + NH4⁺-N) availability increased in ATB amended soils, stayed the same in lime amended soils, and decreased in fly ash amended soils. Availability of PO43–-P was low in all soils but slightly enhanced in ATB amended soils. Fluxes of Cu²⁺, Pb²⁺, Zn²⁺, and Mn²⁺ in amended soils generally decreased over time in association with increased soil pH. Fluxes of Cd²⁺ were not affected by any treatment. Results suggest that ATB is equally as effective as or more effective than lime and fly ash at immediately supplying Ca²⁺, but less effective at supplying Mg²⁺ because of low inputs and cation competition. This suggests that ATB amendments could be an alternative means of quickly adding available Ca²⁺ to Ca-depleted forest soils as long as potential impacts on other nutrient base cations are considered.
... [12] Nitrification, under oxygen conditions, involves the microbial conversion of ammonium to nitrate. It generally increases with an increase in soil pH, but reaches an optimum level at pH 6-8 [13,14]. Denitrification, under limited oxygen conditions, is the microbiological process in which oxidized N species, such as nitrate (NO 3 − ) and nitrite (NO 2 − ), are reduced to gaseous nitric oxide (NO), nitrous oxide (N 2 O), and molecular nitrogen (N 2 ). ...
Crop management and soil properties affect greenhouse gas (GHG) emissions from cropping systems. Irrigation is one of the agronomical management practices that deeply affects soil nitrous oxide (N2O) emissions. Careful management of irrigation, also concerning to soil type, might mitigate the emissions of this powerful GHG from agricultural soils. In the Mediterranean area, despite the relevance of the agricultural sector to the overall economy and sustainable development, the topic of N2O emissions does not have the same importance as N2O fluxes in temperate agricultural areas. Only some research has discussed N2O emissions from Mediterranean cropping systems. Therefore, in this study, N2O emissions from different soil types (sandy-loam and clay soils) were analyzed in relation to the irrigation of a maize crop grown in two contrasting seasons (2009–2010). The irrigation was done using a center pivot irrigation system about twice a week. The N2O emissions were monitored throughout the two-years of maize crop growth. The emissions were measured with the accumulation technique using eight static chambers (four chambers per site). Nitrogen fertilizer was applied in the form of ammonium sulphate and urea with 3,4 dimethylpyrazole phosphate (DMPP) nitrification inhibitors. In 2009, the N2O emissions and crop biomass measured in both soil types were lower than those measured in 2010. This situation was a lower amount of water and nitrogen (N) available to the crop. In 2010, the N2O fluxes were higher in the clay site than those in the sandy-loam site after the first fertilization, whereas an opposite trend was found after the second fertilization. The soil temperature, N content, and soil humidity were the main drivers for N2O emission during 2009, whereas during 2010, only the N content and soil humidity affected the nitrous oxide emissions. The research has demonstrated that crop water management deeply affects soil N2O emissions, acting differently for denitrification and nitrification. The soil properties affect N2O emission by influencing the microclimate conditions in the root zone, conditioning the N2O production.
... In some soils, nitrification and nitrification potential substantially decrease or are negligible below a pH value of 4.2. However, nitrification may still occur even below pH 4.14, suggesting that ammonia-oxidizing and nitrifier communities might remain active at low soil pH [48]. ...
In the natural environment, soil pH has an enormous influence on soil biogeochemical processes. Soil pH is, therefore, described as the “master soil variable” that influences myriads of soil biological, chemical, and physical properties and processes that affect
plant growth and biomass yield. (is paper discusses how soil pH affects processes that are interlinked with the biological, geological, and chemical aspects of the soil environment as well as how these processes, through anthropogenic interventions,
induce changes in soil pH. Unlike traditional discussions on the various causes of soil pH, particularly soil acidification, this paper focuses on relationships and effects as far as soil biogeochemistry is concerned. Firstly, the effects of soil pH on substance
availability, mobility, and soil biological processes are discussed followed by the biogenic regulation of soil pH. It is concluded that soil pH can broadly be applied in two broad areas, i.e., nutrient cycling and plant nutrition and soil remediation (bioremediation
and physicochemical remediation).
... At a pH below 4.5, nitrification is strongly reduced. 253,254 One-half to two-thirds of the total phosphorus is in the organic form and most of the organic-bound phosphorus is created from dead microorganisms. The availability of sulfur depends on the intensity and speed of SOM mineralization. ...
... Class A products are suitable as fertilizer on lawns and gardens [23,24] and recommended for the application to agricultural land as it is assumed to be essentially pathogen-free [25]. In contrast, produced Class B digested sludge can contain an estimated fecal coliform density of over 1,000 cfu/g [26]. The use of Class B biosolids products are more restricted because they contain a detectable level of pathogens. ...
Biosolids are the product of wastewater or municipal solid waste collected through sewerage treatment; the processes of obtaining the biosolids involve various treatment processes, which include digestion, thermal stabilization, thickening, dewatering, and drying, in order to obtain free pathogen granules. These processes undergone by wastewater in the treatment plant ultimately clean the wastewater and remove the solids which are further treated to an acceptable standard for beneficial soil amendments. The application of biosolids are considered to improve soil organic matter, moisture content, and provided essential nutrients, such as nitrogen and phosphorus in arable land as potential plant nutrients supplements for crop optimum yield. Incubation studies on the biosolids-amended soils have shown significant increases in soil phosphorus content being released as plant available P in the soil, and therefore could be a good source of phosphorus in deficient native phosphorus soil. Field-scale experiments on wheat are grown with sewage sludge have also shown yield production comparable to mineral fertilizer-treated soils. This review is thereby aimed at explaining the concept behind the mineralization and mobilization of biosolids phosphorus in soil. In this review paper, an overview of the method of preparations, origin, and sources, its application in agriculture and the environment, chemical composition, the environmental risk, soil amendments potentials of the biosolid sand regulatory, and global perspective of sewage sludge disposal all are reviewed. From the review, it was concluded that mineralization and mobilization of biosolids phosphorus in soil have beneficial input to both environment and soil nutrient amendment. It is thereby recommended that more research studies should be carried out on the mineralization and mobilization of another essential element, such as nitrogen and biochar although more research should be done with respect to mineralization and mobilization of biosolids phosphorus in soil.
... A previous research indicated that soil EC values predict the concentration of soil nitrate because a positive linear regression exists between the two parameters ( Miyamoto et al., 2015). Furthermore, rapid nitrification may occur at low pH leading to accumulation of soil NO 3 − -N and consequently nitrate leaching contributing to low pH values ( Zebarth et al., 2015). This could also have affected the total N content in 2013 since nitrate was leached in drainage water reducing the content of total N in that year. ...
Sesame yield under continuous cropping on upland field converted paddy fields
... The positive and significant relationship was also verified between pH and potential nitrification rate in the soil-biochar mixture of our study (r = 0.713, P<0.01; Table 1). Correspondingly, a large number of studies showed that pH was the most important factor affecting the soil nitrification process and generally low pH was not conducive to nitrification [35][36][37]. ...
Biochar’s production and application in soils has been suggested as a means of abating climate change by sequestering carbon while simultaneously providing energy and increasing crop yields. However, little is known about biochar’s effect on nitrification in alkaline soil. This study focused on the effect of wheat straw-derived biochar (0%, 2%, 5%, and 10%, w/w) on nitrification in a calcareous clay soil with an incubation experiment. Moreover, the variations of ammonia-oxidizing bacteria (AOB) amount, urease activity, pH, and inorganic nitrogen contents during the incubation and their relationships with potential nitrification rates were also explored. The results indicated that nitrification was enhanced by wheat straw-derived biochar and showed an obvious dose-response to biochar application rate. Generally, the potential nitrification rate increased with incubation time elapsing for all four treatments, which were in the ranges of 21.0-33.9, 23.7-45.1, 21.4-57.5, and 31.8-66.1 nmol N/(g dry soil∙h), respectively. The potential nitrification rate increased by 1.36-2.40 times at 10% biochar application rate compared with the control (0%) at the same incubation stage. Except for NH4⁺-N content of the soil-biochar mixture, AOB amount, urease activity, pH, and NO3⁻-N content all showed increasing trends during incubation. Moreover, correlation analysis indicated that the potential nitrification rate was positively correlated with AOB amount, urease activity, pH, and NO3⁻-N content (r≥0.713, P<0.01), but negatively correlated with NH4⁺-N content (r = -0.408, P<0.01). Notably, though the biochar application in the Loess Plateau region has more benefits for soil condition improvement, the enhanced nitrification induced by biochar may pose a negative effect on fertilizer bioavailable efficiency in the agricultural system.
... Relatively higher values of NO 3 -N concentration were observed in the summer and autumn seasons, which were correlated to the amounts of N fertilizer applied and higher nitrification activity due to high temperature in both seasons (Russell et al. 2002). However, the nitrification activities are generally lower in acidic soils (Zebarth et al. 2015), especially at pH values < 5.5 (Kyveryga et al. 2004), but a higher nitrification rate was observed in the experimental soil (pH 4.4). Furthermore, the acid-tolerant nitrifiers have been reported to exist in the acidic soils; they have a potential for high activity as well as for no single factor-controlled nitrification in soil (Yao et al. 2011). ...
The gaseous losses of fertilizer nitrogen (N) applied to agroecosystems are a major contributor to a host of environmental problems, inefficient production systems, and decreased N-use efficiency. These losses lead to the wastage of resources, increasing the greenhouse effect and harming human health. The red soil hilly region of Southeast China houses the biggest orchard area of the world, and nitrogen fertilizers are usually heavily applied to the orchard systems in China. Therefore, this study aimed to measure the gaseous losses of the fertilizer N by ammonia (NH3) volatilization and denitrification losses using the venting method and acetylene inhibition method respectively, and to assess the potential environmental risk of NH3 and nitrous oxide (N2O) emission from this orchard system based on the recent orchard management practices. An experiment was conducted in an Ougan citrus (Citrus reticulata Blanco ‘Suavissima’) orchard in the red soil hilly region of Southeast China. Three fertilization treatments, including the control (no N fertilizer, CK), poultry manure (at a rate of 6.3 t/ha, OM), and conventional fertilization (OM 6.3 t/ha + chemical fertilizer 393 kg N/ha, CF), were used. In all treatments, the fertilizers were incorporated into the soil after application. The test results, which were continuously determined within one year, indicated that the NH3 volatilization losses accounted for 4.5% of the OM nitrogen (OM-N) and 2.9% of the CF nitrogen (CF-N), whereas the denitrification N losses accounted for 2.1% of the OM-N and 2.9% of the CF-N. Overall, the total gaseous N losses (including NH3 volatilization losses and denitrification N losses) were 5.8% in the CF treatment. A relatively higher N2O flux, accounting for 1.8% of the CF-N, emitted from the CF treatment.
... Compounds in cattle manure, such as organic acids with carboxyl and phenolic hydroxyl groups, have an important role in buffering soil acidity and increasing the pH of acidic soils amended with manure (Whalen et al. 2000). Manure may therefore have a neutralizing effect on acidic soils (Table 2), and increased nitrification in these soils may be due to increasing soil pH (Zebarth et al. 2015). ...
The effect of long-term (20 yr) fertilizer application on soil nitrogen (N) transformation in paddy soils was studied at three sites (Xinhua, Ningxiang, and Taojiang) in Hunan province, China. Four fertilization practices were chosen: chemical fertilizers (NPK), chemical fertilizers plus a medium or high amount of pig manure (MM + NPK), chemical fertilizers plus a high amount of pig manure (HM + NPK), and chemical fertilizers plus straw incorporated (Str. + NPK). A treatment with no fertilization was included as a control (CK). Ten week aerobic incubations were conducted to determine N potential mineralization and nitrification. Application of organic plus chemical fertilizer increased soil organic carbon, total nitrogen, and microbial biomass carbon (Cmic) and nitrogen (Nmic), whereas the response of Cmic/Nmic ratio to fertilizer application varied among sites. Across all sites, the HM + NPK treatments had the highest potentially mineralizable N and maximal nitrification rate, and the CK had the lowest. The MM + NPK, Str. + NPK, and NPK treatments had lesser effects on mineralizable N and nitrification. Results indicated that chemical fertilizer along with a high rate of manure application is an effective method to improve available soil N by increasing the N mineralization rate. However, higher N nitrification was also induced by manure application, which may lead to increased N losses, and also should be considered in practical applications.
... Thus 76% of the AOA OTUs could not be classified in this study. In addition, OTU AOA18 was the unique OTU for the NPK treatment, which was further identified as Nitrosotalea sp., of which Nitrosotalea devanaterra is the only cultivated obligatory acidophilic AOA species to date 39 . NPK treatment caused soil acidification resulting in an enrichment of Nitrosotalea sp., demonstrating that pH contributed to variations in the AOA community composition. ...
Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
Ageratina adenophora is an invasive weed species found in many countries. Methods to control the spread of this weed have been largely unsuccessful. Soil pH is the most important soil factor affecting the availability of nutrients for plant and impacting its growth. Understanding the mechanisms of the influence of soil pH on the growth of A. adenophora may help to develop effective control measures. In this study, we artificially changed the soil pH in pot experiments for A. adenophora . We studied the effects of acidic (pH 5.5), weakly acidic (pH 6.5), neutral (pH 7.2), and alkaline (pH 9.0) soils on the growth, availability of soil nutrients, activity of antioxidant enzymes, levels of redox markers in the leaves, and the structure and diversity of the rhizosphere microbiome. Soil with a pH 7.2 had a higher (47.8%) below-ground height versus soils of pH 5.5 at day 10; plant had a higher (11.3%) above-ground height in pH 7.2 soils than pH 9.0 soils at day 90; no differences in the fresh and dry weights of its above- and belowground parts, plant heights, and root lengths were observed in plants growing in acid, alkaline, or neutral pH soil were observed at day 180. Correspondingly, the antioxidant enzymes SOD (superoxide dismutase), POD (peroxidase), CAT (catalase) and redox markers GSH (glutathione) and MDA (malondialdehyde) were measured in the leaves. Significant differences existed in the activities of CAT and the levels of GSH between those growing in acidic and alkaline soils and those in neutral pH soil at day 90; however, only lower (36.8%) CAT activities in those grown at pH 5.5 than those grown at pH 7.2 were found at day 180. Similarly, significant differences in available P (16.89 vs 3.04 mg Kg ⁻¹ ) and total K (3.67 vs 0.96 mg Kg ⁻¹ ), total P (0.37 vs 0.25 g Kg ⁻¹ ) and total N (0.45 vs 1.09 g Kg ⁻¹ ) concentrations were found between the rhizosphere soils of A. adenophora grown at pH 9.0 and 7.2 at day 90; no such differences were seen at day 180. High throughput analyses of the 16S rRNA and ITS fragments showed that the rhizosphere microbiome diversity and composition under different soil pH conditions changed over 180 days. The rhizosphere microbiomes differed in diversity, phylum, and generic composition and population interactions under acid and alkaline conditions versus those grown in neutral soils. Soil pH had a greater impact on the diversity and composition of the prokaryotic rhizosphere communities than those of the fungal communities. A. adenophora responded successfully to pH stress by changing the diversity and composition of the rhizosphere microbiome to maintain a balanced nutrient supply to support its normal growth. The unusual pH tolerance of A. adenophora may be one crucial reason for its successful invasion. Our results suggest that attempts use soil pH to control its invasion by changing the soil pH (for example, using lime) will fail.
In the face of population growth, rising food production costs, limited arable land availability, and farmland environmental degradation, novel technologies are crucial to bolster the resilience of global agri-food systems. Nitrogen-Enriched Organic fertilizer (NEO) is produced using a new method, where dinitrogen (N2) is captured from the air through a plasma process and mixed with bio-based fertilizers as nitrate (NO3-) and nitrite (NO2-). This process leads to solid slurry acidification and a high NO2- content, potentially yielding toxic inorganic or organic N compounds. In this study, we investigated the impact of NEO, derived from cattle slurry and biogas digestate, on soil nitrification, which involves the conversion of NH4+ to NO2- and NO3- by aerobic autotrophic bacteria and archaea. We investigated and compared the potential nitrification rates in soil samples from two agricultural trials (cereal and grass) treated with NEO and other fertilizers after two consecutive fertilization years. Additionally, we examined the immediate nitrification response to NEO through 72-hour bottle incubations. Our results revealed that NEO significantly stimulated nitrification rates in agitated soil slurries, regardless of the feedstock used, surpassing rates observed in ammonium controls. Similarly, this pattern was also observed in loosely placed soil samples, with high nitrification rates occurring with NEO and ammonium chloride. Surprisingly, the differences in nitrification rates between field-fertilized soil samples were minimal and inconsequential, suggesting that while NEO exhibits a rapid boost in nitrification rates shortly after application, this effect is not sustained ≈ six months after fertilization under field conditions. Consequently, NEO indicates its potential as an environmentally benign fertilizer without adversely affecting soil nitrifier communities.
Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in a tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27-34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrient and heavy metal and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced the changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.
Aeration can alleviate soil hypoxia stress of Phyllostachys praecox bamboo under mulching conditions, but how aeration affects soil properties, soil fungal community structure, and bamboo development is unclear. Here we studied the responses of soil properties, fungal community structure, bamboo shoots, and rhizome growth to organic mulching (TM), mulching with aeration (TA1 and TA2), and no‐mulching treatments (CK) from a field experiment in March and July. During the mulching period (March), the better aeration treatment (TA2) improved soil O2 content, bamboo shoots yield and soil nutrient availability significantly compared with TM. TA2 treatment showed significantly higher relative abundances of the genus Trichoderma and functional group endophyte than TM treatment, which might be conducive to soil nutrient transformation and bamboo growth. The TA2 treatment had higher fungal diversity indices than that of the TA1 treatment, suggesting that optimal aeration conditions enhance soil fungal diversity. The fungal community structure also showed strong temporal dynamics in all treatments. Mantel test results indicated soil O2 is the primary factor driving fungal community structure under mulching conditions, while has no impact on the fungal community in summer; fungal community structure was primarily controlled by soil pH in summer. Structural equation model revealed soil NO3‐‐N content was responsible directly for bamboo rhizome growth and shoot yield. Our results indicated short‐term mulching is beneficial to soil nutrients improvement and bamboo yield increase, while rational aeration can further facilitate sustainable plantation development under hypoxic soil conditions. This article is protected by copyright. All rights reserved.
Nonpoint-source nutrients contribute to eutrophication of surface waters. While effects of particular management actions are difficult to identify at the watershed scale, assessing nutrient fluxes over time can illuminate the net impact of trends in land use and management. We investigated nutrient fluxes in upper Kamm Creek in northwest Washington State to determine if historical changes in land management, responding to economic and regulatory shifts, had impacted nutrient export. We compared current (October 2015 to September 2018) nitrogen and phosphorus fluxes in Kamm Creek to data from a previous study (1993 to 1998). We found significantly higher current fluxes of nitrate, and significantly lower current fluxes of orthophosphate (P) and total phosphorus (TP), compared to the historical sampling period. The increased annual nitrate flux resulted from slightly higher average discharge and significantly higher nitrate concentrations throughout the year. In contrast, current P and TP concentrations were significantly lower throughout the year than previously. The Nooksack River, which receives water from the study stream, showed similar patterns for P and TP, but not nitrate. Kamm Creek had reduced phosphorus fluxes and increased nitrate fluxes between the 1993 to1998 and 2015 to 2018 time periods. The watershed experienced several concurrent land-use changes, including reductions in hay and corn acreage, increases in berry crop acreage, legislation to reduce manure application, and altered use of nitrate-enriched groundwater. We cannot currently distinguish among these. Further understanding relationships between specific management changes and nutrient fluxes will help to maintain local agricultural productivity and improve water quality.
Nitrification is a major pathway of N2O production in aerobic soils. Measurements and model simulations of nitrification and associated N2O emission are challenging. Here we innovatively integrated data mining and machine learning to predict nitrification rate (Rnit) and the fraction of nitrification as N2O emissions (fN2ONit). Using our global database on Rnit and fN2ONit, we found that the machine-learning based stochastic gradient boosting (SGB) model outperformed three widely used process-based models in estimating Rnit and N2O emission from nitrification. We then applied the SGB technique for global prediction. The potential Rnit was driven by long-term mean annual temperature, soil C/N ratio and soil pH, whereas fN2ONit by mean annual precipitation, soil clay content, soil pH, soil total N. The global fN2ONit varied by over 200 times (0.006%-1.2%), which challenges the common practice of using a constant value in process-based models. This study provides insights into advancing process-based models for projecting N dynamics and greenhouse gas emissions using a machine learning approach.
Urease inhibitor [N-(n-butyl) thiophosphoric triamide (NBPT)] and nitrification inhibitor [3,4- dimethylpyrazole phosphate (NI)] have been used to reduce nitrogen (N) losses from urea-based fertilizers. This study evaluated the effect of temperature, NBPT, and NI on kinetics and thermodynamics properties of urea hydrolysis in six soils. Soils were amended (250 kg N ha-1) with urea (UR), NBPT treated urea (URNBPT), or NBPT+NI treated urea (URDI); incubated at 5, 15, or 25 oC and destructively sampled eight times during an 18-day incubation. We measured urea hydrolysis rate by the disappearance of urea with time and determined the rate constant (k; d-1) assuming first-order kinetics. Our results showed that k increased with temperature in the order of 0.07 (5 oC), 0.12 (15 oC), and 0.20 (25 oC) across soils and inhibitor treatments. Also, k declined in the order of UR (0.19) > URDI (0.11) > URNBPT (0.08) across soils and temperatures. While urease inhibitor, NBPT, increased the half-life of urea from 3.8 to 8.3 days across soil-temperature, the addition of a NI significantly reduced the half-life of NBPT treated urea by approximately two days across soil-temperature. Thermodynamics parameters showed that urea hydrolysis is nonspontaneous, and enthalpy and entropy changes were not significantly different among inhibitor treatments in five of the six soils. We conclude that the often-reported greater ammonia volatilization from URDI than URNBPT may not only be due to the persistence of ammonium in the presence of NI but also because NI reduced the inhibitory effect of NBPT on urea hydrolysis.
Sesame (Sesamum indicum L.) is an important oilseed crop that is negatively affected by continuous cropping but
there is still limited research on this phenomenon. A three-year field experiment was conducted from 2012 to
2014 at Tottori, Japan, on an upland field converted from a paddy to determine the effect of continuous cropping
on seed yield, crude protein and mineral nutrient contents of four sesame cultivars (‘Maruhime’, ‘Nishikimaru’,
‘Gomazou’, ‘Masekin’) and identify cultivars adaptable to continuous cropping obstacle. Seed yield, crude protein
and mineral nutrient contents were negatively affected in the second cropping: however, the level of response
differed among the cultivars. In the first cropping, the intercultivar yield differences were not significant
whereas seed yield showed significant differences among the cultivars in the second cropping. Averaged over
years, seed yield was significantly lowest in ‘Maruhime’ and ‘Nishikimaru’ compared with ‘Gomazou’ (588.3 kg
ha−1) and ‘Masekin’ (450.3 kg ha−1). Averaged across cultivars, the seed crude protein and N, P, Fe, Zn and Mn
contents decreased by 7.5, 10.0, 19.4, 14.7, and 13.6% in the second cropping compared with the first cropping.
Although ‘Maruhime’ yields in the second cropping were lower than those of the other cultivars, its crude
protein, N, P, and Fe contents were generally highest. Changes in the soil nutrients N and available P partially
explained the decrease in the yield and seed mineral contents. The variation in the seed yield, crude protein and
mineral nutrient contents in the second cropping reflected differences in the cultivar response to continuous
cropping that influence the seed composition. To minimize this yield reduction, adoption of two sesame cultivars
‘Gomazou’ and ‘Masekin’ could be recommended to overcome continuous cropping obstacle on upland fields
converted paddy.
This paper presents the research results of three short-term experiments carried out in 2010–2017 on the impact of green manures and mineral and bacterial fertilizers on potato productivity. The purpose of the study was to increase the productivity and quality of potato tubers while reducing the anthropogenic load on the agrocenosis through the integrated use of binary green manures and lower doses of mineral fertilizers in combination with microbiological preparations. In a stationary field experiment (2010–2012) on leached chernozem, the maximum potato productivity (32.2–35.5 t/ha) was obtained using mineral fertilizers N45–90P60–120K60–120 in the crop rotation link oil radish + vetch–potato, while the efficiency of the treatment of tubers with the bacterial preparations Azotovit + Fosfatovit was 9.2–15.0%. In experiments on sod-podzolic soil, the yield increase from the microbiological preparation Agrinos for the potato cultivar Udacha in 2015 amounted to 12.4% along with higher content of starch and vitamin C in production. In the relatively moist 2016 and 2017, the yield increase in the midearly maturing cultivar Gala reached 8.5 t/ha or 24.5% to the mineral background level (N90P90K90). In the variant with a 30% reduced NPK dose and the use of Agrinos (N60P60K60 + Agrinos A + B (5 + 2.5 L/ha), the yield was 5.8 t/ha or 16.7% higher than with the full dose of NPK, and high starchiness and vitamin C content, excellent culinary qualities, and low levels of nitrates were also observed.
Rooted cuttings of blueberries ( Vaccinium corymbosum L.) were grown in nutrient solutions containing different levels and combinations of NH 4 -N and NO 3 -N. Disappearance rate of the two forms from the nutrient solutions as determined by periodic analysis indicated that the plants absorbed the NH 4 -N more rapidly than NO 3 -N. Although both forms produced healthy plants, the plants receiving NH 4 -N were twice the size and dry matter yield of the NO 3 plants after 15 weeks. Shoot N concentrations ranged from 0.99% to 1.29% for the N forms except where the blueberry plants had depleted the solutions of NH 4 -N before termination of the experiment. The N forms had a significant affect on the concentration of other plant nutrients, notably very low concentrations of Ca and Mg in roots with NH 4 -N and very high concentrations of Mn and Fe in roots with NO 3 -N plants. Expected levels of Mn and Fe and light brown roots were found with NH 4 -N plants.
Highbush blueberries (Vaccinium corymbosum L.) are long lived perennial plants that are grown on acidic soils. The goal of this study was to determine how blueberry cultivation might influence the nitrification capacity of acidic soils by comparing the nitrification potential of blueberry soils to adjacent noncultivated forest soils. The net nitrification potential of blueberry and forest soils was compared by treating soils with 15N enriched (NH4)2SO4, and monitoring nitrate (NO3--N) production during a 34-day incubation period in plastic bags at 18°C. Net nitrification was also compared by an aerobic slurry method. Autotrophic nitrifiers were quantified by the most probable number method. Nitrate production from labeled ammonium (15NH4+) indicated that nitrification was more rapid in blueberry soils than in forest soils from six of the seven study sites. Slurry nitrification assays provided similar results. Blueberry soils also contained higher numbers of nitrifying bacteria compared to forest soils. Nitrification in forest soils did not appear to be limited by availability of NH4+ substrate. Results suggest that blueberry production practices lead to greater numbers of autotrophic nitrifying bacteria and increased nitrification capacity, possibly resulting from annual application of ammonium containing fertilizers.
Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.
Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.
The Abbotsford-Sumas Aquifer is arguably the most studied case in Canada of groundwater nitrate contamination associated with agricultural production. Underlying some of the most productive agricultural land in Canada, this highly vulnerable trans-boundary aquifer provides a unique case study on the opportunities and challenges of addressing water quality issues. A groundwater monitoring program initiated in the early 1990s has been important in tracking spatial and temporal variation in groundwater nitrate concentration. However, small land parcels with spatially and temporally variable land use and management practices and sub-horizontal flow in this highly permeable sand and gravel aquifer make it difficult to relate groundwater monitoring results to specific agricultural practices. Other approaches pointed to the historical over-application of N relative to crop requirement (primarily as manure used to increase soil organic matter during replanting but also as a nutrient source during production). Despite changes in agricultural practices, and programs aimed at raising grower awareness, no appreciable change in average groundwater nitrate concentration has occurred over the monitoring period. On individual land parcels, nitrate contamination may be reduced through development and adoption of an integrated suite of beneficial management practices (BMPs) to improve N fertilization, irrigation and alley vegetation management, and in particular to eliminate application of any organic soil amendment such as untreated manure in which the N has not been stabilized (e.g., by composting). However, the substantial N imbalance on a regional scale, and the lack of an effective on-going consultative process among stakeholders, remain major barriers to the development, demonstration and adoption of BMPs.
Forty acid surface soils of pH 4.0–5.6 were incubated with and without lime, and the amounts of N that were mineralized or nitrified were statistically compared with several soil acidity characteristics. In addition, three field experiments were used to find the effect of liming on N mineralization. There was no relation between the amounts of mineral N released per unit of organic N in 120 days of incubation and soil pH, base saturation or soluble Fe, Al or Mn. Despite this, liming the soils to about pH 6.7 approximately doubled the amounts of N mineralized during incubation. In the field experiments, lime increased uptake of soil N by 15–42 kg/ha in the 1st yr but only 7–10 kg/ha in the 3rd yr. Thus these laboratory and field experiments indicate that soil acidity does not restrict mineralization of organic N and although liming increases mineralization of N, it is generally a temporary effect. Nitrification in the 40 incubated soils occurred much more rapidly in cultivated soils than in virgin soils. For both the virgin and cultivated soils, nitrification decreased with decreasing soil pH. However, nitrification was not statistically related to base saturation or soluble Fe, Al or Mn. Liming established good nitrification in most of the soils and this effect did not diminish with time.
The effect of soil pH on rates of ammonification and nitrification was studied. Soil samples which ranged in pH from 4.7 to 6.6 from an established lime and N fertility experiment were used. Soil pH values in the lime plots have been relatively constant for several years. Soil pH did not affect rates of ammonification appreciably; however it had a significant effect on nitrification rates. Length of the delay period ( t ′) was increased and rate of NO 3 ‐ accumulation (Km) decreased with a decrease in soil pH. Previous field N treatments increased the length of t ′ at low pH and decreased t ′ and Km at high pH. Nitrification rates and production of NO 3 ‐ were similar for soil pH values of 5.3, 6.0, 6.3, and 6.6 with a different pattern at pH 4.7.
The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea-amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water-amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time-course incubations indicated that archaeal amoA genes were increasingly labelled by (13) CO(2) in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the (13) C-DNA, and acetylene inhibition suggests that autotrophic growth of urease-containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a-associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear.
Most of our knowledge about the physiology of ammonia-oxidizing bacteria is based on experiments with Nitrosomonas europaea, which appears to be less ubiquitous than Nitrosospira. We have isolated Nitrosospiras from widely different environments and compared their specific growth rate, substrate affinity, urease activity, temperature response, pH tolerance and cell morphology. Two of the strains had a variable morphology: the spirals were less tightly coiled than the classical Nitrosospira type and a fraction of the culture had a vibrioid appearance. These vibrioid strains were also peculiar in having a much higher apparent activation energy for ammonia monooxygenase (AMO) (129 and 151 kJ mol−1) than that of the more classical Nitrosospiras (78 and 79 kJ mol−1). The differences in morphology and activation energy were congruent with the phylogeny of the genes for 16S rRNA (Utåker et al., System. Appl. Microbiol. 18) and AMO. The response to pH in the medium was investigated for four strains. The oxidation rate at the onset of the pH exposure experiment was found to obey classical steady state enzyme kinetics, assuming that NH3 (not NH4+) is the rate-limiting substrate. The calculated half saturation constants (Ks) for AMO were 6–11 μM NH3. Growth had a narrower pH range than oxidation activity and appeared to be restricted by pH-dependent factors other than NH3. All the isolated strains were urease positive, with a specific urease activity ranging from 60 to 158% of their specific AMO activity. The urease activity was unaffected by acetylene inhibition of the energy metabolism. The substrate affinity for one strain was found to be around 670 μM.
Nitrification in acid soils was first reported in the beginning of the 20th century. Although this finding has been well substantiated by countless studies since then, it has until recently remained unclear which micro-organisms were responsible for nitrate production at low pH. Substantial evidence now supports the role of chemolitho–autotrophic bacteria as the main nitrifying agents in most acid soils. Heterotrophs may make some contribution to nitrification in acid soils, but this is difficult to demonstrate conclusively. Current insights in the phylogenetic position of autotrophic nitrifying bacteria in acid soils and the mechanisms that may enable them to be active at low pH are presented. In addition, the spatial variability of their activity and their contribution to the flux of the greenhouse gas N2O is discussed.
Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.
Forest fertilization in British Columbia is increasing, to alleviate timber shortfalls resulting from the mountain pine beetle epidemic. However, fertilization effects on soil microbial communities, and consequently ecosystem processes, are poorly understood. Fertilization has contrasting effects on ammonia-oxidizing bacteria and archaea (AOB and AOA) in grassland and agricultural ecosystems, but there are no studies on AOB and AOA in forests. We assessed the effect of periodic (6-yearly application 200 kg N ha⁻¹) and annual (c. 75 kg N ha⁻¹) fertilization of lodgepole pine and spruce stands at five long-term maximum productivity sites on potential nitrification (PN), and the abundance and diversity of AOB, AOA and Nitrobacter and Nitrospira-like nitrite-oxidizing bacteria (NOB). Fertilization increased AOB and Nitrobacter-like NOB abundances at some sites, but did not influence AOA and Nitrospira-like NOB abundances. AOB and Nitrobacter-like NOB abundances were correlated with PN and soil nitrate concentration; no such correlations were observed for AOA and Nitrospira-like NOB. Autotrophic nitrification dominated (55–97%) in these forests and PN rates were enhanced for up to 2 years following periodic fertilization. More changes in community composition between control and fertilized plots were observed for AOB and Nitrobacter-like NOB than AOA. We conclude that fertilization causes rapid shifts in the structure of AOB and Nitrobacter-like NOB communities that dominate nitrification in these forests.
The present study describes the occurrence of a unique archaeal ammonia monooxygenase alpha subunit (amoA) gene in nitrifying acid-sulfate soil microcosms at pH 3.5. The soil was collected from an abandoned paddy field in Thailand. Microcosms were incubated in the dark at 30°C for 372 days with the following three treatments: addition of ammonium sulfate solution once a month (I) or once a week (II), and addition of only sterilized water (III). A quantitative PCR analysis revealed an increase in abundance of the archaeal amoA gene in microcosm soils in which nitrate concentrations increased after incubation. A phylogenetic analysis indicated a predominance of the novel gene, and a predominance of a betaproteobacterial amoA gene affiliated with the genus Nitrosospira. A 16S rRNA gene-based PCR assay revealed that crenarchaeotic Group I.1d was predominant among the Crenarchaeota in microcosms. These results suggest the presence of ammonia-oxidizing archaea corresponding to the unique amoA lineage in nitrifying acid-sulfate soil microcosms at pH 3.5.
Nitrification is a central component of the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in terrestrial ecosystems by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Published studies indicate that soil pH may be a critical factor controlling the relative abundances of AOA and AOB communities. In order to determine the relative contributions of AOA and AOB to ammonia oxidation in two agricultural acidic Scottish soils (pH 4.5 and 6), the influence of acetylene (a nitrification inhibitor) was investigated during incubation of soil microcosms at 20 °C for 1 month. High rates of nitrification were observed in both soils in the absence of acetylene. Quantification of respective amoA genes (a key functional gene for ammonia oxidizers) demonstrated significant growth of AOA, but not AOB. A significant positive relationship was found between nitrification rate and AOA, but not AOB growth. AOA growth was inhibited in the acetylene-containing microcosms. Moreover, AOA transcriptional activity decreased significantly in the acetylene-containing microcosms compared with the control, whereas no difference was observed for the AOB transcriptional activity. Consequently, growth and activity of only archaeal but not bacterial ammonia oxidizer communities strongly suggest that AOA, but not AOB, control nitrification in these two acidic soils.
Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.
We have conducted a preliminary phylogenetic survey of ammonia-oxidizing beta-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing beta-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonas-like sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types.
Most Vaccinium species have strict soil requirements for optimal growth, requiring low pH, high iron availability and nitrogen primarily in the ammonium form. These soils are limited and are often located near wetlands. Vaccinium arboreum is a wild species adapted to a wide range of soils, including high pH, low iron, and nitrate-containing soils. This broader soil adaptation in V. arboreum may be related to increased efficiency of iron or nitrate uptake compared with the cultivated Vaccinium species.
Nitrate, ammonium and iron uptake, and nitrate reductase (NR) and ferric chelate reductase (FCR) activities were compared in two Vaccinium species grown hydroponically in either nitrate or ammonia, with or without iron. The species studied were the wild V. arboreum and the cultivated V. corymbosum interspecific hybrid, which exhibits the strict soil requirements of most Vaccinium species.
Ammonium uptake was significantly greater than nitrate uptake in both species, while nitrate uptake was greater in the wild species, V. arboreum, compared with the cultivated species, V. corymbosum. The increased nitrate uptake in V. arboreum was correlated with increased root NR activity compared with V. corymbosum. The lower nitrate uptake in V. corymbosum was reflected in decreased plant dry weight in this species compared with V. arboreum. Root FCR activity increased significantly in V. corymbosum grown under iron-deficient conditions, compared with the same species grown under iron-sufficient conditions or with V. arboreum grown under either iron condition.
V. arboreum appears to be more efficient in acquiring nitrate compared with V. corymbosum, possibly due to increased NR activity and this may partially explain the wider soil adaptation of V. arboreum.
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