Abundance Of Ammonia-oxidizing Archaea Research Articles

The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China.

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.

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.

Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China

Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg−1 as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.

Developing antibiotics-based strategies to efficiently enrich ammonia-oxidizing archaea from wastewater treatment plants

The effects of five antibiotics (i.e., ampicillin, streptomycin, carbenicillin, kanamycin and tetracycline) on ammonia-oxidizing archaea (AOA) enrichment from anoxic activated sludge were investigated. The combined use of five antibiotics during 90-day cultivation could selectively inhibit nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB) with AOA unaffected, as evidenced by the nitrite accumulation ratio of 100 % and the proportion of AOA in ammonia-oxidizing microbes over 91 %. The alternative use of five antibiotics was the optimal approach to screening for AOA during 348-day cultivation, which inhibited AOB growth at a level equivalent to the combined use of five antibiotics (the AOB-amoA gene decreased by over 99.90 %), further promoted AOA abundance (the much higher AOA-amoA to AOB-amoA gene copy number ratio (1453.30) than that in the groups with the combined use of five antibiotics (192.94)), eliminated bacterial adaptation to antibiotics and reduced antibiotic-resistant bacteria to form Nitrocosmicus-dominant community (42.35 % in abundance).

Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.

Studies publishedrecently proposed that ammonia-oxidizing archaea (AOA) may bebeneficial for hypersaline (salinity > 50g NaCl L-1) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L-1 in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance tothe challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.

The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected via q-PCR microbial abundance measurement.

Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off-target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co-operation and Development, which is a key international standard-setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5-dichloraniline). We determined the following in three different soils: (i) ammonium (NH4 +) and nitrate (NO3 -) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia-oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q-PCR). All pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose-dependent effects on NH4 + and NO3 - levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q-PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5-dichloraniline. Our findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well-standardized tools. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China.

Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

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.

Local climate conditions explain the divergent climate change effects on (de)nitrification across the grassland biome: A meta-analysis

Ecosystem functions, such as soil nitrogen cycling, are being altered by climate change. The responses of soil (de)nitrification to climate change are different and sometimes opposite across global grasslands. However, it remains unclear how the local environmental conditions and the duration and magnitude of climate change experiments influence these responses. We synthesized the results of 49 studies corresponding to 518 observations on the effects of warming, elevated CO2, and elevated precipitation, and unfolded the reasons for the divergent responses in (de)nitrification to these climate change factors. We found that the responses of (de)nitrification are mainly related to annual precipitation and temperature, and less to the duration and magnitude of experimental treatment. In contrast, soil variables such as pH and organic carbon had no significant effects on these responses. Specifically, the effect of warming on the abundance of ammonia-oxidizing archaea (AOA) shifted from negative for mean annual precipitation (MAP) < 600 mm to positive for MAP>700 mm, whereas the effects on denitrification decreased with mean annual temperature (MAT). The effects of elevated CO2 on nitrification, denitrification and soil nitrate all decreased with MAP, with negative effects observed for MAP>700 mm. The effects of elevated P on nitrification and soil ammonium decreased with MAP, with negative effects observed for MAP>300 mm. The results suggested that in dry regions, altered water availability governs climate change effects, while changed nitrogen availability is likely the main determinant in wet regions. This shows how biochemical models should include local climatic conditions when predicting nitrogen dynamics across the grassland biome under future climate change scenarios.

Tree species richness and functional composition drive soil nitrification through ammonia-oxidizing archaea in subtropical forests

Understanding the links between plant diversity and functional microbiota is crucial for unraveling the mechanisms by which plant communities regulate ecosystem functions. However, the underlying mechanism of how tree diversity influences soil nitrification remains elusive in forest ecosystems. Here we investigated the impacts of tree species richness and their functional composition (including functional identity and functional trait diversity) on the dynamics of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and arbuscular mycorrhizal (AM) fungi using a tree diversity experiment established with 32 native tree species in a subtropical forest biome. Our study revealed that tree species richness had a positive concave-down relationship with the abundance of AOA. Furthermore, the community-weighted mean of leaf nitrogen and specific root length were significant positive factors for the abundances of AOA and AOB, respectively. By contrast, functional trait diversity of specific root length was negatively associated with the biomass of AM fungi. Regression analysis showed that the abundance of AOA was positively correlated with soil net nitrification rates, while the biomass of AM fungi was negatively correlated with soil net nitrification rates. The structural equation model showed that the positive effect of leaf nitrogen on nitrification was driven by the increase in AOA. By contrast, the functional trait diversity of specific root length indirectly increased soil nitrification via a negative impact on the biomass of AM fungi. Taken together, our findings demonstrate that both tree species richness and tree functional composition promoted soil nitrification by increasing the AOA abundance, and emphasize the key role of the interplay between tree diversity and functional microbiota in predicting ecosystem functions.

Nitrification in the water column of Lake Erie: Seasonal patterns, community dynamics, and competition with cyanobacterial harmful algal blooms

Abstract This study reports directly measured nitrification rates in the water column of western Lake Erie, which is affected by annual cyanobacterial harmful algal blooms, and across all three Lake Erie basins. Over three field seasons, 15NH4+ stable isotope tracers were employed to quantify nitrification rates, and relative abundances of ammonia-oxidizing bacteria and ammonia-oxidizing archaea were determined via qPCR. Nitrification rates ranged from undetectable to 1,270 nmol L-1 d-1 and were generally greatest in the western basin near the Maumee River mouth (a major nutrient source). Nitrification rates were highest in early summer, and often lowest during peak cyanobacterial harmful algal blooms months (August and September), before increasing again in October. In the western basin, nitrification was negatively correlated with cyanobacterial biomass. There were no consistent differences in nitrification rates between the three Lake Erie basins. Over the three years in western Lake Erie, ammonia-oxidizing bacteria and ammonia-oxidizing archaea were often present in high and similar abundances, but overall, ammonia-oxidizing bacteria exceeded ammonia-oxidizing archaea, particularly in 2017. No relationships were observed between nitrification rates and ammonia-oxidizing bacteria and ammonia-oxidizing archaea abundances. Thus, despite abundant ammonia-oxidizer DNA, lower nitrification rates during cyanobacterial harmful algal blooms suggest that nitrifiers were poor competitors for regenerated and available NH4+ during these blooms, as also observed in similar systems. Low nitrification rates during cyanobacterial harmful algal blooms could limit system nitrogen removal via denitrification, a natural pathway for its removal and a valuable ecosystem service. Lower denitrification rates allow more bioavailable nitrogen to remain in the system and support biomass and microcystin production; therefore, these results help explain how non-nitrogen-fixing cyanobacterial harmful algal blooms persist, despite low bioavailable nitrogen concentrations during these blooms, and support management efforts to reduce external nitrogen loading to eutrophic systems.

Ammonia-oxidizing archaea bacteria (AOB) and comammox drive the nitrification in alkaline soil under long-term biochar and N fertilizer applications

Ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia oxidizers (comammox) take an essential part in soil nitrogen (N) cycling. In case of 8 years biochar and N fertilizer application, nevertheless, the comparative contribution of comammox, AOA and AOB to nitrification is unclear. Our long-term field study on alkaline soil (pHwater 8.49) investigated the impact of biochar and N fertilizer on nitrification rate and potential ammonia oxidation in terms of the soil properties, both physical and chemical, together with the abundance and diversity of AOA, AOB and comammox. The findings revealed that biochar and N fertilizer did not affect the amoA abundance of AOA but increased it in AOB and commamox clade A and clade B, but decreased the diversity of AOA and comammox. Nitrogen fertilization significantly declined the diversity of AOB. The AOB abundance was controlled mainly by pH, whereas the AOA, AOB and comammox Chao1 index were governed by soil microbial biomass carbon (MBC). Additionally, biochar increased the soil nitrification rate with or without N fertilizer, but N fertilizer decreased the soil nitrification rate and potential ammonia oxidation (with nitrite oxidation inhibited) under the same biochar application. Biochar and/or N fertilizer increased the corresponding contribution of AOA and comammox to ammonia oxidation by 143–156 % and 33–395 %, respectively, but suppressed the contribution of AOB. Although the abundance of AOA amoA was obviously greater than that of AOB and comammox, the highest contribution to ammonia oxidation was by AOB in soil not fertilized by N and by comammox in the N-fertilized soil. Our findings suggest that changes in soil properties brought about by biochar and N fertilizer addition can influence the diversity of AOA, AOB and comammox, affecting potential ammonia oxidation and the nitrification rate. The AOB and comammox make a bigger contribution to nitrification than AOA in the alkaline soil.

Comammox plays a functionally important role in the nitrification of rice paddy soil with different nitrogen fertilization levels

Chemoautotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizers (comammox) catalyze ammonia oxidation; however, quantifying their individual gross ammonia oxidation activities in complex soil ecosystems remains elusive. In this study, we investigated the nitrifying population and community dynamics in response to fertilization in paddy soil under long-term treatment with different urea concentrations (0, 100, 200, and 300 kg N ha−1; designated N0, N100, N200, and N300, respectively). The community structure of nitrifiers, including comammox, was changed by long-term N fertilizers input, which also enhanced AOB abundance and comammox clade A/B abundance ratio, whereas it did not affect AOA abundance. Nevertheless, the microbial population sizes and community compositions remained largely similar following short-term fertilization throughout one rice-growing season. Furthermore, by employing a 15NO3− pool dilution technique in combination with chlorate and 1-octyne inhibition, we conducted a soil microcosm incubation without substrate supplementation to distinguish the relative contribution of comammox to gross ammonia oxidation from those of AOA and AOB. Comammox exhibited higher nitrification activity in soils treated with more N fertilizers, with the contribution increasing from 34 % (N0) to 75 % (N300), although its abundance was not dominant. This could be attributed to the repeated N-based fertilization, which reduced the soil pH, thereby decreasing the soil-free ammonia concentration. In contrast, the contribution of AOA declined from 57 % (N0) to 19 % (N300), while that of AOB only accounted for a minor fraction (<25 %) despite being in high abundance. Altogether, our findings provide evidence that the activity of nitrifying guilds is more valuable than their abundance and provide insights into the potential functional significance of comammox in the nitrification process in rice paddy systems.

Organic Material Addition Optimizes Soil Structure by Enhancing Copiotrophic Bacterial Abundances of Nitrogen Cycling Microorganisms in Northeast China

Using organic fertilizer and maize straw as friendly amendment measures is effective for altering soil nitrogen (N) cycling in farmlands. However, the synthetical effects of organic fertilizer combined with straw returning on soil quality remain unknown, especially in response to soil nitrification and denitrification microorganisms. We set up an experiment in brunisolic soil from Northeast China, mainly including four treatments: CK (no addition without traditional chemical fertilizer), O (organic fertilizer application), S (straw returning), and OS (organic fertilizer combined with straw returning). The soil nitrification and denitrification microorganisms were further investigated using high-throughput sequencing. Our results show that, compared to CK, the soil water content, field capacity, macroaggregates with a diameter &gt; 0.25 mm, mean weight diameter, total carbon, total nitrogen, ammonium, nitrate, microbial biomass carbon, and microbial biomass nitrogen were significantly improved, and penetration resistance was reduced in a 0–20 cm soil layer under O, S, and OS treatments. Moreover, OS treatment effectively increased the available potassium and available phosphorus content and decreased the three-phase R-value. The application of organic fertilizer and straw effectively optimized the soil structure, especially the OS treatment. Compared to CK, O, S, and OS treatments had a higher abundance of ammonia-oxidizing archaea (AOA) and further enhanced the alpha diversity and lower abundance of ammonia-oxidizing bacteria (AOB) and nirK-, nirS-, and nosZ-type denitrifying microbes. AOA and nirK were the key drivers of the ammonia oxidation process and nitrite reduction process, respectively. Meanwhile, the application of organic fertilizer and straw regulated the relative abundance of Nitrososphaeria (AOA), Gammaproteobacteria (nirK and nirS), Alphaproteobacteria (nirK), and Betaproteobacteria (nirS) in the soil. Organic fertilizer and straw returning regulated the soil structure by enhancing the abundance of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria in the nitrifying and denitrifying microorganism communities. Taken together, OS treatment was a suitable straw-returning practice for optimizing the nutrient balance of the farmland ecosystem in Northeast China. However, this study did not determine how to reduce traditional nitrogen fertilizer applications under organic fertilizer application and straw returning; therefore, we aim to carry out related research in future works.

Effects of nitrification and urease inhibitors on ammonia-oxidizing microorganisms, denitrifying bacteria, and greenhouse gas emissions in greenhouse vegetable fields

Soil microorganisms and N cycling are important components of biogeochemical cycling processes. In addition, the study of the effects of nitrification and urease inhibitors on N and microorganisms in greenhouse vegetable fields is essential to reducing N loss and greenhouse gas emissions. The effects of nitrification inhibitors [2-chloro-6-(trichloromethyl) pyridine (CP), dicyandiamide (DCD)], and urease inhibitor [N-(n-butyl) thiophosphoric triamide (NBPT)] on soil inorganic N (NH4+-N, NO2−-N and NO3−-N) concentrations and the production rates of greenhouse gases (N2O, CH4, and CO2) in greenhouse vegetable fields were investigated via indoor incubation experiments. Polymerase chain reaction amplification and high-throughput sequencing technology (Illumina Miseq) were used to explore the community structure and abundance changes of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifying bacteria (nirK and nirS). The results showed that CP and DCD obviously inhibited NH4+-N conversion, and NO2−-N, and NO3−-N accumulation, NBPT slowed down urea hydrolysis and NH4+-N production, and the apparent nitrification rates of soil were in the following order: NBPT > DCD > DCD + NBPT > CP + NBPT > CP. Compared with urea treatment, the peak N2O production rate of inhibitor treatment decreased by 73.30–99.30%, and the production rate of CH4 and CO2 decreased by more than 66.16%. DCD and CP reduced the abundance of AOA and AOB, respectively. Furthermore, NBPT hindered the growth of ammonia-oxidizing microorganisms and nirS-type denitrifying bacteria, and urea and nitrification inhibitors were detrimental to the growth of Ensifer and Sinorhizobium in the nirK community. Nitrification and urease inhibitors can effectively slow down nitrification and greenhouse gas emissions, reduce N loss and improve soil quality by inhibiting the growth of ammonia-oxidizing microorganisms and denitrifying bacteria.

Accelerated nitrification and altered community structure of ammonia-oxidizing microorganisms in the saline-alkali tolerant rice rhizosphere of coastal solonchaks

Plantations of saline-alkali tolerant rice in coastal areas are proposed as a strategy to improve rice yield and ensure global food security. The soil nitrification process driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is an integral part of the soil nitrogen cycle and correlates with the quality of coastal solonchak. However, little is known about the effects of saline-alkali tolerant rice cultivation on the soil nitrification process in coastal solonchaks. In this study, we investigated the community structures of AOA/AOB and the nitrification rate in the rice rhizosphere along salinity gradients. The abundance and nitrification rates of AOA and AOB declined with increasing salinity. Saline-alkali-tolerant rice cultivation significantly increased the abundance of AOA and AOB amoA genes from (3.09–11.5) × 106 and (7.76–52.0) × 105 copies g−1 in soils to (16.2–50.9) × 106 and (69.2–423) × 105 copies g−1 in the rhizosphere, respectively. Compared with bulk soils, the nitrification rate of AOA and AOB in the rhizosphere increased significantly with salinity. Saline-alkali-tolerant rice cultivation enhanced the nitrification process of saline-alkali tolerant soil by increasing the nitrification contribution of AOB. Our findings offer new clues on the accelerated nitrification process in the saline-alkali tolerant rice rhizosphere in coastal solonchaks and reveal its roles in shaping AOA/AOB communities, providing suggestions for saline-alkali tolerant rice plantations in coastal solonchaks.

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.

Threshold responses of soil gross N transformation rates to aridity gradient.

The responses of soil nitrogen (N) transformations to climate change are crucial for biome productivity prediction under global change. However, little is known about the responses of soil gross N transformation rates to drought gradient. Along an aridity gradient across the 2700 km transect of drylands on the Qinghai-Tibetan Plateau, this study measured three main soil gross N transformation rates in both topsoil (0-10 cm) and subsoil (20-30 cm) using the laboratorial 15 N labelling. The relevant soil abiotic and biotic variables were also determined. The results showed that gross N mineralization and nitrification rates steeply decreased with increasing aridity when aridity was less than 0.5 but just slightly decreased with increasing aridity when aridity was larger than 0.5 at both soil layers. In topsoil, the decreases of the two gross rates were accompanied by the similar decreased patterns of soil total N content and microbial biomass carbon with increasing aridity (p<0.05). In subsoil, although the decreased pattern of soil total N with increasing aridity was still similar to the decreases of the two gross rates (p<0.05), microbial biomass carbon did not change (p>0.05). Instead, bacteria and ammonia oxidizing archaea abundances decreased with increasing aridity when aridity was larger than 0.5 (p<0.05). With an aridity threshold of 0.6, gross N immobilization rate increased with increasing aridity in wetter region (aridity<0.6) accompanied with an increased bacteria/fungi ratio, but decreased with increasing aridity in drier region (aridity>0.6) where mineral N and microbial biomass N also decreased at both soil layers (p<0.05). This study provided new insight to understand the differential responses of soil N transformation to drought gradient. The threshold responses of the gross N transformation rates to aridity gradient should be noted in biogeochemical models to better predict N cycling and manage land in the context of global change.

Arbuscular mycorrhizal fungi reduce ammonia emissions under different land-use types in agro-pastoral areas

Ammonia (NH3) emissions, the most important nitrogen (N) loss, always induce a series of environmental problems such as increased the frequency of regional haze pollution, accelerated N deposition, and N eutrophication. Arbuscular mycorrhizal (AM) fungi play key roles in N cycling. However, whether AM fungi can alleviate N losses by reducing NH3 emissions is still unclear. The potential and mechanism by which AM fungi reduce NH3 emissions in five land-use types (grazed grassland, mowed grassland, fenced grassland, artificial alfalfa grassland, and cropland) were explored in this study. The results showed that AM fungal inoculation significantly reduced NH3 emissions and the mycorrhizal responses of NH3 emissions were determined by land-use type. Structural equation modeling (SEM) showed that AM fungi and land-use type directly affected NH3 emissions. In addition, the reduction in NH3 emissions was largely driven by the decline in soil NH4+-N and pH and the increase the abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), urease activity and plant N content induced by AM fungal inoculation and land-use type. The present results highlight that reducing the negative influence of agricultural intensification caused by land-use type changes on AM fungi should be considered to reduce N losses in agriculture and grassland ecosystems.