Ammonia-oxidizing Bacteria Population Research Articles

Soil moisture modulates biological nitrification inhibitors release in sorghum plants

Background and aimsSorghum (Sorghum bicolor) is able to exude allelochemicals with biological nitrification inhibition (BNI) capacity. Therefore, sorghum might be an option as cover crop since its BNI ability may reduce N pollution in the following crop due to a decreased nitrification. However, BNI exudation is related to the physiological state and development of the plant, so abiotic stresses such as drought might modify the rate of BNI exudation. Hence, the objective was to determine the effect of drought stress on sorghum plants’ BNI release.MethodsThe residual effects of sorghum crops over ammonia-oxidizing bacteria (AOB) were monitored in a 3-year field experiment. In a controlled-conditions experiment, sorghum plants were grown under Watered (60% WFPS) or Moderate drought (30% WFPS) conditions, and fertilized with ammonium sulphate (A), ammonium sulphate + DMPP (A+D), or potassium nitrate (KNO3−). Soil mineral N was determined, and AOB populations were quantified. Additionally, plant biomass, isotopic discrimination of N and C, and photosynthetic parameters were measured in sorghum plants.ResultsIn the driest year, sorghum was able to reduce the AOB relative abundance by 50% at field conditions. In the plant-soil microcosm, drought stress reduced leaf photosynthetic parameters, which had an impact on plant biomass. Under these conditions, sorghum plants exposed to Moderate drought reduced the AOB abundance of A treatment by 25% compared to Watered treatment.ConclusionThe release of BNI by sorghum under limited water conditions might ensure high soil NH4+-N pool for crop uptake due to a reduction of nitrifying microorganisms.

Manure combined with biochar reduces rhizosphere nitrification potential and amoA gene abundance of ammonia-oxidizing microorganisms in acid purple soil

Fertilization and soil environmental factors determine the niche differentiation of ammonia-oxidizing microorganisms, thereby affecting the ammonia-oxidation process. However, the characteristics of rhizosphere potential nitrification rate (PNR), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) population under manure combined biochar are unclear. In this study, a pot experiment growing lemon was conducted, setting up six treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), manure combined with biochar (MBC), fresh manure combined with biochar (FMBC). We investigated the effects of manure, chemical fertilizer and manure combined with biochar on soil physical-chemical properties, PNR, and the amoA gene abundance, diversity and structure of AOA and AOB in the rhizosphere. Our results showed that compared with CK treatment, CF and CFBC increases PNR by 19.3–34.7 % in the rhizosphere, M, MBC and FMBC decrease PNR about 60.0 %; CF and CFBC increased AOA amoA gene copies by 40.2–101.7 %, while M, MBC and FMBC treatments decreased it by 66.5–81.9 %, five fertilization treatments decreased the AOB amoA gene copy by 33.1–81.9 %. The redundancy analysis showed that chemical fertilizer and manure combined with biochar affects the population structure of AOA and AOB by pH, available phosphorus (AP), ratio of carbon to nitrogen (C/N), soil moisture content (SMC), nitrate nitrogen (NO3−-N) and ammonium nitrogen (NH4+-N) in the rhizosphere. The results of partial least squares indicated that pH, total nitrogen (TN), AOA amoA gene copy and AOA Shannon index were main factors affecting nitrification potential in the rhizosphere. Therefore, AOA dominates the ammonia oxidation process in the acid purple soil under the condition of chemical fertilizer and pig manure combined with rice husk biochar. Meanwhile, fertilization affected ammonia oxidation process by regulating soil pH and TN in lemon rhizosphere soil.

Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil

Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Elevated loading rates as a low operational intensity and small land footprint design strategy to achieve partial nitritation

An urgent need exists for cost-effective, low operational intensity and small land footprint ammonia treatment systems to meet stringent wastewater discharge regulations. A moving bed biofilm reactor system operating under a novel design strategy using elevated total ammonia nitrogen (TAN) loading rates ranging from 3 to 6.5 g TAN/m2·d has shown promise to achieve robust partial nitritation (PN) and the oxidation of TAN with limited oxidation of nitrite without the need for intense operational measures. An investigation of the biofilm, the viability of the embedded cells and the microbial ecology is necessary to fully understand this low operational intensity design. The investigation revealed that, at a loading rate of 6.5 g TAN/m2·d, the abundance of nitrite oxidizing bacteria (NOB) was 2 ± 0.46%; however, the NOB activity was negligible with 99 ± 0.2% nitrite accumulation; thus, the mechanism to attain robust PN is shown to be the suppression of NOB activity as opposed to NOB population suppression. This decrease in NOB activity is associated with an increase in thickness and mass of the biofilm, as well as the relative increase in ammonia oxidizing bacteria (AOB) that preferentially uptake oxygen compared to NOB. As such, this design strategy results in the suppression of the NOB activity due to limited access to oxygen via mass transfer limitations through thick biofilm and competition with an augmented AOB population in the biofilm. This research presents a low operational intensity and small footprint PN strategy that can be an effective alternative to more intensive strategies.

Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary

Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Cyanotoxin impact on microbial-mediated nitrogen transformations at the interface of sediment-water column in surface water bodies

Harmful cyanobacterial blooms produce lethal toxins in many aquatic ecosystems experiencing eutrophication. This manuscript presents results on the effects of cyanotoxins on the aerobic microbial communities residing at the interface of sediments and water columns with the ammonia-oxidizing bacteria (AOB) as the model microbial community. Microcystin-LR (MC-LR), a heavily researched cyanotoxin variant, was used as the model cyanotoxin. To measure cyanotoxin influence on the activity of nitrifying microbial communities, an enriched culture of AOBs collected from an ongoing partial nitrification-nitritation reactor was examined for its exposure to 1, 5 and 10 μg/L of MC-LR. The nitritation kinetics experiment demonstrated MC-LR’s ability at 1, 5, and 10 μg/L concentrations to prevent ammonium oxidation with statistically significant differences in nitritation rates between the blanks and spiked samples (One-way ANOVA, p < 0.05). Significantly decreased dissolved oxygen (DO) consumption during oxygen update batch tests demonstrated toxin’s influence on AOB’s oxidizing capabilities when exposed to even lower concentrations of 0.75, 0.5, and 0.25 μg/L of MC-LR in a separate set of experiments. Based on competitive kinetics, the MC-LR inhibition coefficient-the concentration needed to produce half-maximum inhibition of the mixed community AOBs was determined to be 0.083 μg/L. The stress tests proved the recovery of nitritation to some extent at lower MC-LR concentrations (1 and 5 μg/L), but significant irreversible inhibition was recorded when the AOB population was exposed to 10 μg/L MC-LR. The comparisons of amoA gene expressions corresponded well with nitrifying kinetics. All concentrations of MC-LR spiking were determined to produce a discernible impact on the AOB nitritation rate by either destroying the bacterial cell or immediately inhibiting the amoA gene expression.

Bentonite-Based Organic Amendment Enriches Microbial Activity in Agricultural Soils

Bentonite-based organic amendments may have the potential to enhance soil microbial properties. The experiment was carried out from 2014 to 2017 comprising four treatments: NPK fertilizer (nitrogen, phosphorus and potassium mineral fertilizer as a control), NPK + cattle manure, NPK + bentonite, and NPK + combination of manure with bentonite (MB) to verify this hypothesis. The effect of treatments on seven different soil microbial properties was measured: dehydrogenase activity (DHA), bacterial phospholipid fatty acid content, fungal phospholipid fatty acid content, microbial biomass carbon (Cmic), 16S rDNA, 18S rDNA, and ammonia-oxidizing bacteria in soil. The results showed that solely bentonite treatment increases the bacterial and fungal biomass, which was further confirmed by the increased 16S rDNA and 18s rDNA gene copy numbers. The only significantly decreased values upon treatment with solely bentonite were recorded for DHA and Cmic. The ammonia-oxidizing bacteria population increased with the sole application of bentonite and reached its maximum value when bentonite was applied with manure. The MB treatment showed the highest value for all seven measured properties. In summary, the application of bentonite solely might increase or decrease the soil activity, but its addition, along with manure, always promotes an abundance of soil microorganisms and their activity. The co-application of bentonite with manure altered the soil microbial properties in a 3-year field experiment in favor of increased microbial biomass, which is beneficial for agriculture and environment and reveals the potential for the restoration of polluted lands.

Lost in translation: the quest for Nitrosomonas cluster 7-specific amoA primers and TaqMan probes.

The choice of primer and TaqMan probes to quantify ammonia-oxidizing bacteria (AOB) in environmental samples is of crucial importance. The re-evaluation of primer pairs based on current genomic sequences used for quantification of the amoA gene revealed (1) significant misrepresentations of the AOB population in environmental samples, (2) and a lack of perfect match primer pairs for Nitrosomonas europaea and Nitrosomonas eutropha. We designed two new amoA cluster 7-specific primer pairs and TaqMan probes to quantify N. europaea (nerF/nerR/nerTaq) and N. eutropha (netF/netR/netTaq). Specificity and quantification biases of the newly designed primer sets were compared with the most popular primer pair (amoA1f/amoA2r) using DNA from various AOB cultures as individual templates as well as DNA mixtures and environmental samples. Based on the qPCR results, we found that the newly designed primer pairs and the most popular one performed similarly for individual templates but differed for the DNA mixtures and environmental samples. Using the popular primer pair introduced a high underestimation of AOB in environmental samples, especially for N. eutropha. Thus, there is a strong need for more specific primers and probes to understand the occurrence and competition between N. europaea and N. eutropha in different environments.

The Contribution of Root Turnover on Biological Nitrification Inhibition and Its Impact on the Ammonia-Oxidizing Archaea under Brachiaria Cultivations

Aims: Biological nitrification inhibition (BNI) has been reported as an emerging technology to control soil nitrifier activity for effective N-utilization in cropping systems. Brachiaria have been reported to suppress nitrifier populations by releasing nitrification inhibitors from roots through exudation. Substantial BNI activity has been reported to be present in the root tissues of Brachiaria grasses; however, BNI contribution, such as root turnover, has not been addressed in previous studies. The present study aimed to clarify the contribution of root turnover on BNI under Brachiaria cultivations and its impact on nitrifier populations. Methods: We monitored root growth, changes in ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) numbers, nitrification rate, and available nitrogen (N) content under seven germplasm lines of Brachiaria, for 18 months with seasonal profile sampling. Results: Brachiaria cultivation increased soil NH4+-N, available N, and total soil carbon levels. Though we did not find any correlation between the changes in AOB populations and potential nitrification, the potential nitrification rate decreased when AOA populations decreased. Multiple regression analysis indicated that BNI substances from root tissue turnover had a significant contribution to the BNI function in the field. Conclusion Results indicated that the inhibitory effect of BNI was mostly evident in AOA, and not in AOB, in this study. Brachiaria cvs. ‘Marandu’, ‘Mulato’, and ‘Tupy’ had the most substantial BNI effect among the seven cultivars evaluated. The estimated total BNI activities and available N content of root tissue explained the observed nitrification inhibition. In conclusion, the release of BNI substances through plant decomposition contributes to the decrease in the abundance of AOA, and thus the inhibition of nitrification under Brachiaria cultivation.

Long-Term Effects of Biochar-Based Organic Amendments on Soil Microbial Parameters

Biochar application to the soil has been recommended as a carbon (C) management approach to sequester C and improve soil quality. Three-year experiments were conducted to investigate the interactive effects of three types of amendments on microbial biomass carbon, soil dehydrogenase activity and soil microbial community abundance in luvisols of arable land in the Czech Republic. Four different treatments were studied, which were, only NPK as a control, NPK + cattle manure, NPK + biochar and NPK + combination of manure with biochar. The results demonstrate that all amendments were effective in increasing the fungal and bacterial biomass, as is evident from the increased values of bacterial and fungal phospholipid fatty acid analysis. The ammonia-oxidizing bacteria population increases with the application of biochar, and it reaches its maximum value when biochar is applied in combination with manure. The overall results suggest that co-application of biochar with manure changes soil properties in favor of increased microbial biomass. It was confirmed that the application of biochar might increase or decrease soil activity, but its addition, along with manure, always promotes microbial abundance and their activity. The obtained results can be used in the planning and execution of the biochar-based soil amendments.

Impact of Dicyandiamide (DCD) and 3,4-Dimethylpyrazole Phosphate (DMPP) on Ammonia-oxidizing Bacteria and Archaea in a Vegetable Planting Soil

Nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) showed significant effects in the inhibition of nitrification and the improvement of the utilization efficiency of nitrogen fertilizer in agricultural soils. However, the effects of different NIs on ammonia-oxidizing bacteria (AOB) and archaea (AOA) is still unclear. To verify the inhibitory effect of DCD and DMPP on AOB and AOA, a pot experiment was performed, including Urea, Urea+DCD, and Urea+DMPP treatments. The dynamics of NH4+-N and NO3--N and nitrification potential among different treatments were measured. In addition, real-time PCR and high-throughput sequencing approaches were applied to investigate the changes in the AOB and AOA population abundance and composition. The results revealed that the concentrations of NH4+-N in Urea+DCD and Urea+DMPP treatments were 213% and 675% higher than that in the CK treatment, respectively. However, the concentrations of NO3--N and the nitrification potentials were 13.3% and 37.2%, and 20.4% and 82.4% lower than that in CK treatment, respectively; Furthermore, the copy numbers of the bacterial and archaeal amoA gene were 51.2% and 56.5%, and 6.0% and 27.0% lower than that in the CK treatment, respectively. However, the diversity indexes of AOB and AOA communities, including evenness and richness, exhibited no significant differences after addition of DCD and DMPP. The nork-environmental-samples, unclassified-Nitrosomonadaceae, unclassified-Bacteria, and Nitrosospira, were the predominant genera of the AOB community. The no rank-Crenarchaeota, no rank-environmental-samples and Nitrososphaera were the predominant groups in the AOA community. Summarily, application of DCD and DMPP significantly delayed the transformation of NH4+-N, decreased the formation of NO3--N, inhibited the abundance and changed the composition of AOB and AOA communities. DMPP had a stronger inhibitory effect on nitrification, and on AOB and AOA than DCD. Therefore, compared with DCD, DMPP had a better application prospect regarding the improvement of the nitrogen utilization efficiency in vegetable soil.

High-rate partial-nitritation and efficient nitrifying bacteria enrichment/out-selection via pH-DO controls: Efficiency, kinetics, and microbial community dynamics.

Conventional nitrification/denitrification process is gradually being replaced with partial-nitritation/anammox (PN/A) processes due to its installation and running cost. However, high ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria activity as well as optimum out-selection of nitrite-oxidizing bacteria (NOB) are necessary to achieving efficient PN/A process. Consequently, to enhance PN process via nitrifying bacteria enrichment/out-selection within psychrophilic environment, a novel pH-DO (dissolved oxygen) control strategy was proposed and the response of PN, kinetics, AOB enrichment, and NOB out-selection efficiency was investigated during start-up and long-term operation. With DO of 0.7 mg/L and pH of 7.5-7.9, quick start-up of the PN process was established within 34d as NO2--N accumulation ratio (NAR) reached 90.08 ± 1.4%. Again, when NLR was elevated to 0.8 kg/m3·d (400mgNH4+-N/L), DO curtailed to 0.2 mg/L, pH maintained at 7.7 and free ammonium at 6.5 mg/L, NAR and NH4+-N removal rate could still reach 97.04 ± 2.4% and 97.84 ± 1.5%, respectively. After optimum control factors had been established, real nitrogen-rich-mine-wastewater was fed (DO, 0.2 mg/L, pH, 8.9, and free ammonia, 6.5 mg/L) and NAR and NH4+-N removal rate reached was 97.33 ± 0.5% and 97.76 ± 1.1%, respectively. Estimated kinetic parameters including maximum degradation rate (Vmax = 1.58/d), half-rate constant (Km = 33.8 mg/L), and inhibition constant (Ki = 201.6 mg/L) suggested that inhibition on NH4+-N oxidation was most feasible at higher concentration of NH4+-N. To elucidate biological mechanisms, 16S rRNA high-throughput revealed that AOB (Nitrosomonas) enrichment had increased from 0.08% to 49% whereas NOB (Nitrospira) abundance reduced from 1% to 0.034%, indicating pH-DO control efficiently enriched AOB and out-selected NOB. Conversely, when influent NH4+-N was curtailed to about 200 mg/L and free ammonia concentration maintained at 6.5 mg/L, the population of AOB was observably reduced by 6% within a period of 14 days, indicating control strategies including pH-DO control and substrate availability were the key factors which substantially influenced and promoted the activities and growth of AOBs in the present SBR.

Beneficial dual role of biochars in inhibiting soil acidification resulting from nitrification

The dual role of biochar for inhibiting soil acidification induced by nitrification was determined through two-step incubation experiments in this study. Ca(OH)2 or biochar was added respectively to adjust soil pH to the same values (pH 5.15 and 5.85), and then the amended soils were incubated in the presence of urea for 70 days. The results showed that compared with Ca(OH)2 treatment, both rice straw biochar and peanut straw biochar inhibited the decrease in soil pH and the increase in exchangeable acidity during the incubation. The application of biochars suppressed soil nitrification during the incubation, and thus reduced 7.5 mmol kg−1 and 1.4 mmol kg−1 protons released from nitrification compared to Ca(OH)2 treatments. Compared with Ca(OH)2 treatment, the ammonia-oxidizing bacteria population size was decreased by 8% and 12% in rice straw biochar and peanut straw biochar treatments respectively, which was the main responsibility for the inhibited nitrification after biochar application. In addition, the application of rice straw biochar and peanut straw biochar increased soil pH buffering capacity (pHBC) respectively by 22% and 32%. The increased pHBC played the main role (75%) in inhibiting the acidification of the soil amended with peanut straw biochar, while the rice straw biochar inhibited soil acidification mainly through suppressing nitrification during the incubation. Overall, compared with lime application, biochars can inhibit soil acidification caused by urea application through suppressing the nitrification process and improving the resistance of soils to acidification. The crop residue biochars presented a longer-lasting effect on ameliorating acidic soils than mineral lime.

Responses of nitrification and denitrification to nitrogen and phosphorus fertilization: does the intrinsic soil fertility matter?

Nitrogen (N) is not only a major regulator of productivity in terrestrial systems but can also be a pollutant. While the effects of fertilizer addition to soil N cycling processes and the associated soil microbial groups have been extensively studied, little attention has been paid to the interaction of fertilizer amendment and the intrinsic fertility of the soil. We conducted a filed study on the Chinese Loess Plateau with soils of two fertility levels (low fertility and high fertility), amended with or without synthetic fertilizer (N and phosphorus, NP). Soil samples were collected three times in a continuous winter wheat cropping system and analyzed for soil potential nitrification (PNA) and denitrification (DEA) rates, nitrifiers and denitrifiers. Populations of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and the resulting PNA were increased by the NP application regardless of intrinsic soil fertility. The NP application increased DEA by 15–228% in the low fertility soil, but decreased DEA by 18–46% in the high fertility soil. Soil denitrifiers also showed divergent responses to NP application in low and high fertility soils, i.e., the abundance of nirS-nitrite reducers increased in the low fertility soil, while nirS- and nirK-nitrite reducers were unchanged in the high fertility soil. The narG-nitrate reducers, AOB and AOA were more responsive to the NP application in the tillering stage (BBCH 25–26) than in other periods, whereas PNA, DEA and denitrifier gene abundance (nirS and nirK) varied more in the flowering stage (BBCH 65). Our results suggest that the responses of soil nitrification/nitrifiers and denitrification /denitrifiers to NP application varied with intrinsic soil fertility levels. The contrasting responses of nitrification and denitrification to NP application in high fertility soil indicate a decoupling of both processes.

Insights into functional microbial succession during nitrogen transformation in an ectopic fermentation system

The ectopic fermentation system (EFS) is an advanced technology for treating farm wastewater, and it reduces ammonia nitrogen emission and nitrogen loss of fermentation products. This study observed the functional bacteria succession related to nitrogen metabolism in EFS by high throughput sequencing, and evaluated their associations with environmental factors. Results revealed that with the changes of temperature, pH, moisture content, and nitrogen content during fermentation, the species richness and diversity of ammonia oxidizing bacteria (AOB) with amoA increased, but those of denitrifying bacteria carrying nirK and nosZ decreased. During the fermentation process, the dominant bacterial populations of AOB and denitrifying bacteria changed significantly, and different bacterial populations showed different positive/negative correlations with the environmental factors. This study revealed the role of functional bacteria in ammonia removal and nitrogen conservation of EFS, and provided a theoretical basis for the improvement of microbial agents and EFS application.

Spatial and temporal responses of ammonia-oxidizing bacteria and archaea to organic amendments in rice-wheat rotation system

To determine the effects of organic amendment on communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in rice-wheat rotation ecosystem, a long-term plot experiment with 5 treatments was conducted, and the temporal dynamics (10 growth stages) and spatial distribution (0–100 cm) of AOB and AOA abundance were determined using qPCR. The five treatments were as follows: no fertilizer control (CK), regular fertilization (RT), straw returning (SR), straw biochar returning (SB) and organic-chemical mixed fertilization (MF). The results showed the following. 1) Organic addition did not affect the temporal dynamics of AOB abundance but altered those of AOA abundance. Relative to RT, SR and MF significantly lowered AOB population sizes across the 10 sampling time points by 34.49% and 16.42%, respectively, whereas no significant differences in total AOA population size were observed among the 4 fertilization regimes. 2) Compared with the other treatments, treatments involving organic addition had higher total AOB abundance in the 0–100 cm soil layer. However, SB was the only treatment with organic addition that had a significantly higher total AOA abundance than RT (by 24.91%). 3) Under organic addition, the potential nitrification rate (PNR) was still highly correlated with AOB abundance (P < 0.01) but not AOA abundance.

Biochar reduces the efficiency of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) mitigating N2O emissions

Among strategies suggested to decrease agricultural soil N2O losses, the use of nitrification inhibitors such as DMPP (3,4-dimethylpyrazole phosphate) has been proposed. However, the efficiency of DMPP might be affected by soil amendments, such as biochar, which has been shown to reduce N2O emissions. This study evaluated the synergic effect of a woody biochar applied with DMPP on soil N2O emissions. A incubation study was conducted with a silt loam soil and a biochar obtained from Pinus taeda at 500 °C. Two biochar rates (0 and 2% (w/w)) and three different nitrogen treatments (unfertilized, fertilized and fertilized + DMPP) were assayed under two contrasting soil water content levels (40% and 80% of water filled pore space (WFPS)) over a 163 day incubation period. Results showed that DMPP reduced N2O emissions by reducing ammonia-oxidizing bacteria (AOB) populations and promoting the last step of denitrification (measured by the ratio nosZI + nosZII/nirS + nirK genes). Biochar mitigated N2O emissions only at 40% WFPS due to a reduction in AOB population. However, when DMPP was applied to the biochar amended soil, a counteracting effect was observed, since the N2O mitigation induced by DMPP was lower than in control soil, demonstrating that this biochar diminishes the efficiency of the DMPP both at low and high soil water contents.

Effects of adding readily available carbon to soil on nitrogen losses from cattle urine patches

ABSTRACT A lysimeter experiment was carried out to investigate the effects of applying readily available carbon (12 or 24 t sucrose ha−1) to soil on nitrogen (N) losses from cattle urine patches. The carbon (C) was readily available to microbes and was applied onto intact soil monolith lysimeters, containing stony silt loam soil, beneath either ryegrass (Lolium perenne)/white clover (Trifolium repens) pasture (RG/WC) or lucerne (Medicago sativa). Cow urine (700 kg N ha−1) was applied in early July 2017, two days after C application. The application of readily available C increased the immobilisation of N in the soil which reduced the amount of soil mineral N. The C-induced immobilisation of N reduced the ammonia oxidising bacteria population growth rate and the amount of nitrate leached by 51–89%. The addition of readily available C had no significant effect on nitrous oxide emissions. These findings were consistent under both RG/WC and lucerne.