Ammonia-oxidizing Bacteria Community Research Articles

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Stability of ammonia oxidizer communities upon nitrogen fertilizer pulse disturbances is dependent on diversity

Diversity of the soil microbial community is an important factor affecting its stability against disturbance. However, the impact of the decline in soil microbial diversity on the stability of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is not known, particularly considering the repeated soil nutrient disturbances occurring in modern agricultural systems. Here, we conducted a microcosm experiment and modified the soil microbial diversity using the dilution-to-extinction approach to determine the stability and population dynamics of AOB and AOA communities with repeated nitrogen (N) fertilizer application. Our results demonstrated that the AOB community became more abundant and stable against repeated disturbances by N in the treatments with the highest microbial diversity. In contrast, the abundance of AOA decreased following repeated N fertilizer application, regardless of the microbial diversity. Notably, during the initial application phase, AOA displayed a potential for increased abundance in treatments with high soil microbial diversity. These findings highlight that the soil microbial diversity controls the stability of ammonia oxidizers during short-interval repeated N disturbances.

The impact of fertilization on ammonia-oxidizing bacteria and comammox Nitrospira communities and the subsequent effect on N2O emission and maize yield in a semi-arid region.

The control of nitrous oxide (N2O) emissions through nitrification and the optimization of maize yield are important in agricultural systems. However, within the semi-arid region, the impact of fertilization on the function of nitrification communities and its connection with N2O emissions in the rhizosphere soil is still unclear. Our study investigates the influence of fertilization treatments on the communities of ammonia-oxidizing bacteria (AOB) and the complete ammonia oxidizers of the Nitrospira known as comammox (CAOB) in a maize agroecosystem. Nitrous oxide production, potential nitrification activity (PNA), maize yield, and nitrogen use efficiency (NUE) were determined for the same samples. The fertilizer treatments included a control group without fertilization (NA), inorganic fertilizer (CF), organic fertilizer (SM), combined inorganic and organic fertilizer (SC), and maize straw (MS). The SC treatment indicated a lower cumulative N2O emission than the CF treatment in the 2020 and 2021 cropping seasons. The AOB community under the CF, MS, and SM treatments was predominantly composed of Nitrosospira cluster 3b, while the SC treatment was associated with the comammox Nitrospira clade A.1 lineage, related to key species such as Ca. Nitrospira inopinata and Ca. Nitrospira nitrificans. Network analysis demonstrated a positive potential for competitive interaction between hub taxonomy and distinct keystone taxa among AOB and comammox Nitrospira nitrifiers. The structural equation model further revealed a significant positive association between AOB nitrifiers and N2O emission, PNA, soil pH, SOC, -N, and DON under organic fertilization. The keystone taxa in the comammox Nitrospira nitrifier and network Module II exhibited a positive correlation with maize productivity and NUE, likely due to their functional activities stimulated by the SC treatment. It is noteworthy that the AOB community played a more significant role in driving nitrification compared to the composition of comammox Nitrospira. Collectively, combined inorganic and organic fertilizer (SC) treatment exhibits high potential for reducing N2O emissions, enhancing maize productivity, increasing NUE, and increasing the sustainability of the nitrogen dynamics of maize agroecosystems in the semi-arid Loess Plateau.

Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China

Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg−1 N ha−1) was 23.35 % higher than that at the intermediate rate (100–150 kg−1 N ha−1) and 20.77 % higher than that at the low rate (< 100 kg−1 N ha−1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.

Ammonia-oxidizing bacteria are the primary N2O producers in long-time tillage and fertilization of dryland calcareous soil

Human intervention in agriculture, such as tillage and fertilization, could result in major changes of N2O emissions that understanding the N2O emission mechanism is of great significance in reducing the N2O emissions of the agricultural system. In this work, we focused on the conventional tillage practice and straw return practice used in the spring maize production system of this region and compared them by the addition of 3,4-dimethylpyrazole phosphate (DMPP) to explore the N2O emission mechanism of the farmland. Compared with conventional farming, straw return significantly increased the N2O emissions from the soil. Soil pH had important effects on soil N2O emissions through its influence on the ammonia oxidizer community. In addition, DMPP was used to distinguish N2O emissions driven by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and the results showed that AOB were the dominant factor regulating N2O emissions after receiving nitrogen from an external source in dryland farming calcareous soil. Through the analyses of soil AOB community composition and the aggregated boosted tree (ABT) model for N2O emissions, Nitrosospira Cluster 3a.2 was found to be the main driving force of soil N2O emissions in AOB communities. These findings will help better understand the physiochemical and biological mechanisms underlying the N2O emissions of agricultural soils and provide insight for reducing the negative impact of agricultural production systems on the ecological environment.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0–6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3−-N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3−-N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3−-N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

Spatial distribution of ammonia oxidizers in marine sediments of the Bohai, Yellow and East China Seas

Ammonia oxidation, an essential process within the global nitrogen cycle, is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). To date, the current knowledge on the biogeography of AOA and AOB in the ocean across a large geographic distance remains poorly known. In this study, the abundance, microbial composition, and diversity of AOA and AOB in marine sediments collected from the Bohai Sea, Yellow Sea, and East China Sea were characterized by employing quantitative PCR and Illumina Miseq sequencing of both archaeal and bacterial amoA genes. qPCR analysis demonstrated significantly higher abundances of archaeal amoA genes than those of bacterial amoA genes with AOA/AOB ratios varying from 1.59 to 292.88, suggesting a greater contribution of AOA to nitrification in the seas. Nitrosopumilus and Nitrosospira were the predominant clusters of AOA and AOB respectively in all sediment samples. The distribution pattern of both AOA and AOB communities revealed by PCoA (principal coordinate analysis) showed distinct geographic separation of sediment samples from the three seas. Correlation analysis indicated that ammonia (NH4+-N) and nitrate (NO3−-N) content were the main selective forces leading to the distinct biogeography of the two ammonia oxidizers in the ocean. The results are of great significance in improving our understanding of the contribution of AOA and AOB in the nitrogen transformation in the marine ecosystem and providing insights into the environmental factors that shape the assembly of aerobic ammonium oxidizers.

Gross nitrogen transformations and ammonia oxidizers affected by nitrification inhibitors and/or organic amendments in a calcareous soil: A 15N tracing study

Nitrification inhibitors (NIs) combined with organic amendments are considered effective strategies for improving soil nitrogen availability and reducing nitrogen loss. However, these effects might depend on the types of organic amendments and nitrification inhibitors, and whether their combined application could generate a synergistic effect on nitrogen transformation rate has not been well investigated. In this study, a 15N aerobic incubation experiment was conducted to investigate the effects of nitrification inhibitors (3,4-dimethylpyrazole phosphate [DMPP, 1 % of applied NH4+-N] or methyl 3-(4-hydroxyphenyl) propionate [MHPP, 5 % of applied NH4+-N]) and/or organic amendments (straw [1 %, w/w] or straw-derived biochar [1 %, w/w]) on the gross nitrification rates of mineralization, nitrification, and immobilization in calcareous soil. Our findings revealed that compared with the control treatment, biochar, straw, and MHPP_straw boosted gross mineralization rates by 1.19–2.69 times. The addition of nitrification inhibitors and/or organic amendments inhibited the gross nitrification rates by 15.8 %–89.7 %, which ranged from 0.85 mg N kg−1 day−1 to 8.28 mg N kg−1 day−1 across treatments. DMPP_straw showed the greatest inhibiting effect, whereas 5 % MHPP treatment had the least effect. Gross NH4+ immobilization rates increased by 4.12–18.18 times, where NO3− immobilization rates were only stimulated with the treatments of straw, DMPP_straw, and MHPP_straw. DMPP was more efficient in inhibiting nitrification than MHPP, but it also significantly enhanced ammonia (NH3) volatilization, which rose by 2.77 times over that in MHPP. The high C/N ratio and inorganic-N adsorption of straw and biochar might play prominent roles in affecting NH4+ content by stimulating mineralization and inorganic immobilization. The decrease in the abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) can be partially explained by the inhibitory effects of DMPP and MHPP. Changes in the community of AOB were more sensitive to management measures than those of AOA. In conclusion, our study demonstrates that treatments with DMPP_straw and MHPP_straw efficiently promote inorganic nitrogen immobilization, mitigate NH3 volatilization, inhibit nitrification to the greatest extent, and thus yield the most positive synergistic effects on soil nitrogen retention.

Seed treatment with plant-defense elicitors decreases the abundance of ammonia oxidizers associated with winter wheat roots

Priming with elicitors, including phytohormones, is known to induce physiological changes in plants that affect resource allocation and nutrient uptake strategies. However, effects of these changes on belowground microbial communities, particularly those involved in nitrogen (N) transformations, remain poorly characterized. Here, we tested the hypothesis that treating seeds with elicitors would affect N-transforming communities associated to roots and rhizosphere, influencing soil N availability and thus plant performance. We measured the effects of treating winter wheat seeds with cis-jasmone, methyl jasmonate or methyl salicylate on plant traits and on the genetic potential for ammonia oxidation by ammonia-oxidizing bacteria (AOB) and archaea (AOA), the initial inorganic N transformation process resulting in N loss. Elicitors reduced the genetic potential for ammonia oxidation by AOB in root-associated microbial communities and increased traits reflecting N uptake in winter wheat. Proposed mechanisms include increased exploitative competition for ammonium, limiting substrate availability for microorganisms, and induced biological nitrification inhibition capacity actively suppressing ammonia oxidizers. There were minor effects on the composition of the AOB and AOA communities, but an indicator species analysis showed that several AOB and a few AOA genotypes were indicative of elicitor treatments. Seed treatment with elicitors may represent an overlooked strategy to minimize nitrification to mitigate N losses from arable soils.

Rational utilization of urease and nitrification inhibitors improve the ammonia-oxidizing bacteria community, nitrogen use efficiency and peanut growth

ABSTRACT Peanuts (Arachis hypogaea L.) is an important oil and nitrogen (N) fixing crop. Urease inhibitors (UIs) and nitrification inhibitors (Nis) can mitigate the release of N and reduce the harmful effects of excessive N concentrations. However, the effect of these inhibitors on the soil nutrient-microbial activity-plant growth system is unknown in peanut. The purpose of this study was to investigate the effects and mechanism of N-(n-butyl) thiophosphoric triamide (NBPT), 3,4-dimethylpyrazole phosphate (DMPP) and sulfur-coated urea (SCU) on peanut. The results showed that comparing with urea alone, adding NBPT + DMPP inhibited the urea hydrolysis better and decreased the concentration of NH4 +-N + NO3 −-N by 20.8% in soil. Therefore, it increased the net photosynthetic rate, promoted the development of roots even the absorption of N by peanut, with N use efficiency (NUE) up to 20.8%. The effect of NBPT + DMPP on microorganism was better than that of NBPT alone, which considerably impacted the structure and abundances of aonia oxidizing bacteria (AOB) but not ammonia-oxidizing archaea (AOA). Specifically, g_Nitrosospira and g_Nitrosomonas decreased by 46.9% and 2.2% respectively, and g(c) Betaproteobacteria increased. Furthermore, when combined with SCU on this basis, the overall effect was clearer.

Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils

Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.

Limited dissolved oxygen facilitated nitrogen removal at biocathode during the hydrogenotrophic denitrification process using bioelectrochemical system

Effects of limited dissolved oxygen (DO) on hydrogenotrophic denitrification at biocathode was investigated using bioelectrochemical system. It was found that total nitrogen removal increased by 5.9%, as DO reached about 0.24 mg/L with the cathodic chamber unplugged (group R_Exposure). With the presence of limited DO, not only the nitrogen metabolic pathway was influenced, but the composition of microbial communities of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were enriched accordingly. After metagenomic analysis, enriched genes in R_Exposure were found to be associated with nearly each of nitrogen removal steps as denitrification, nitrification, DNRA, nitrate assimilation and even nitrogen fixation. Moreover, genes encoding both Complexes III and IV constituted the electron transfer chain were significantly enriched, indicating that more electrons would be orientated to the reduction of NO2–-N, NO-N and oxygen. Therefore, enhanced nitrogen removal could be attained through the co-respiration of nitrate and oxygen by means of NH4+-N oxidation.

Proper organic substitution attenuated both N2O and NO emissions derived from AOB in vegetable soils by enhancing the proportion of Nitrosomonas

The ammonia oxidation process driven by microorganisms is an essential source of nitrous oxide (N2O) and nitric oxide (NO) emissions. However, few evaluations have been performed on the changes in the community structure and abundance of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under substituting portion of chemical fertilizers with organic manure (organic substitution) and their relative contribution to the ammonia oxidation process. Here, five long-term fertilization strategies were applied in field (SN: synthetic fertilizer application; OM: organic manure; M1N1: substituting 50 % of chemical N fertilizer with organic manure; M1N4: substituting 20 % of chemical N fertilizer with organic manure; and CK: no fertilizer). We investigated the response characteristics of AOB and AOA community structures by selective inhibitor shaking assays and high-throughput sequencing and further explained their relative contribution to the ammonia oxidation process during three consecutive years of vegetable production. Compared to SN and M1N4, the potential of ammonia oxidation (PAO) was significantly reduced by 26.4 % and 22.3 % in OM and 9.5 % and 4.4 % in M1N1, resulting in N2O reductions of 38.9 % and 30.8 % (OM) and 31.2 % and 21.1 % (M1N1), respectively, and NO reductions of 45.0 % and 34.1 % (OM) and 40.1 % and 28.3 % (M1N1). RDA and correlation analyses showed that the soil organic carbon and ammonium nitrogen content increased while AOB gene abundance and diversity significantly decreased with increasing organic replacement ratio; however, the relative abundance of Nitrosomonas in AOB increased in OM and M1N1, which further demonstrates that AOB are the main driver in vegetable soils. Therefore, the appropriate proportion of organic substitution (OM and M1N1) could decrease the N2O and NO emissions contributed by AOB by affecting the soil physicochemical properties and AOB community structure.

The activity of ammonia-oxidizing bacteria on the residual effect of biochar-compost amended soils in two cropping seasons

Ammonia-oxidizing bacteria (AOB) are vital in regulating nitrification in agricultural soils. Nevertheless, the knowledge of the AOB community's response to fortified and composted biochar application in the maize/soybean agroecosystem is scarce. This study examined the residual effects of a control soil (CNZ), biochar (BIZ), compost (CPZ), composted biochar (CBZ), and fortified biochar (FBZ) on the AOB community composition, soil chemical properties, and enzyme activities in 2018 and 2019 of a maize/soybean agroecosystem. The AOB community was unravelled using Illumina Miseq sequencing, and multivariate approaches were used to explain the data collected. In 2018, FBZ increased the content of NO3--N, while CPZ, CBZ, and FBZ improved total nitrogen (TN) in the soil. In 2019, CBZ and FBZ increased NO3--N content, while CPZ improved TN and NO2--N in the soil. Likewise, CPZ significantly differed from FBZ, CBZ, and BIZ in AOB richness, while CBZ significantly differed from BIZ in AOB diversity in 2019. Furthermore, distance-based redundancy analysis (db-RDA) and Spearman correlation showed a significant correlation with NH4+-N and NO2--N in 2018 and TN and NO3--N in 2019, while Nitrosomonas eutropha and Nitrosomonas nitrosa had the highest weighted degree in the co-occurrence network in both years. This research demonstrates that co-application of biochar with compost in the maize/soybean agroecosystem could result in changes in the AOB community structure.

Long-term enclosure at heavy grazing grassland affects soil nitrification via ammonia-oxidizing bacteria in Inner Mongolia

Enclosure and grazing can significantly change the turnover of nitrogen in grassland soil. Changes of soil nitrogen mineralization and ammonium-oxidizing microorganisms caused by enclosure in different grazing intensities (about 30 years of grazing history) grassland, however, has rarely been reported. We selected the grassland sites with high and medium grazing intensity (HG and MG, 4 and 2 sheep ha−1, respectively) and had them enclosed (45 × 55 m) in 2005 while outside the enclosure was continuously grazed year-round. A two factorial study was designed: grazing intensity (MG and HG sites) and enclosure (fence and non-fence). Nitrogen mineralization was detected through a laboratory incubation experiment. The abundance and community structure of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed using quantitative PCR (q-PCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning, and sequencing. Results showed that compared with MG site, at HG site the AOB abundance and community structure of AOB changed significantly while the AOA abundance and community structure did not change obviously. Enclosure significantly decreased the cumulative mineralized N, N mineralization rate, the abundance of AOB and the AOB community structure at the HG site, while at MG site, enclosure did not change these parameters. Potential nitrification rate (PNR) was positively correlated with the abundance of AOA and AOB at the MG and HG sites, respectively. The abundance of AOA was significantly correlated with soil pH; however, AOB abundance was significantly correlated with soil available N, total N, C/N ratio, pH, etc. The phylogenetic analysis showed that Nitrososphaeraceae and Nitrosomonadaceae were the dominant AOA and AOB, respectively. Totally, the responses of AOB and AOA mainly were associated to changes in soil physicochemical properties caused by different intensity grazing; AOB and AOA may be the dominant functional players in ammonia oxidation processes at HG and MG site, respectively.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Effect of gradual increase of atmospheric CO2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields

Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.