Abundance Of Ammonia-oxidizing Bacteria Research Articles

Ammonia-oxidizing bacteria-driven autotrophic nitrification dominated nitrous oxide production in calcareous soil under long term plastic film mulching

Fertilized cropland soils are a major source of anthropogenic N2O emissions in terrestrial ecosystems. However, the main N2O production pathways and microbes underlying N2O production in calcareous cropland soil under long-term plastic film mulching and nitrogen (N) management have not yet been clarified. Here, we used 15N tracing combined with quantitative polymerase chain reaction to evaluate the relative contributions of different N2O production pathways (i.e., autotrophic nitrification, heterotrophic nitrification, and denitrification) to N2O production in a calcareous maize field soil; we also used specific inhibitors (acetylene and 1-octyne) to determine the functional importance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to N2O production. Autotrophic nitrification accounted for 47–63% and 76–100% of total N2O emissions in unfertilized (F0) and N-fertilized soils, respectively. AOB accounted for 62% and 91–98% of total N2O production in F0 and N-fertilized soils, respectively. N2O production was significantly lower in soils following long-term film mulching (F225) compared with the bare land soil (N225), and this was due to the reduced abundance and activity of AOB and N2O derived from autotrophic nitrification. Autotrophic nitrification-derived N2O emissions were 2.2-fold, 3.6-fold, and 6.3-fold higher in the F225 treatment (appropriate N level), the treatment in which the level of N was the same as that applied by local farmers (F380), and the manure addition treatment (F225+M) compared with F0, respectively, indicating that autotrophic nitrification was the main driver of increases in N2O emissions. These findings provide the first direct evidence showing that AOB-driven autotrophic nitrification is the dominant N2O production pathway in the plastic film mulched calcareous soils under different agricultural management practices. Our results also show that autotrophic nitrification is depressed by long-term mulching and promoted by N fertilization. These findings have implications for the development of targeted N2O mitigation strategies.

Responses of biofilm communities in a hybrid moving bed biofilm reactor-membrane bioreactor system to sulfadiazine antibiotic exposure

Antibiotics in wastewater can affect the structures and functions of bacterial communities, subsequently influencing how well a biological process performs. Therefore, the characteristics of bacterial community were investigated in a hybrid moving bed biofilm reactor-membrane bioreactor system when treating domestic wastewater containing sulfadiazine (SDZ). Results indicated total nitrogen removal reduced by 10.2%, 9.1%, 2.7% and 2.9%, respectively, with increasing carbon to nitrogen (C/N) ratios (2.5, 4, 6 and 9) when SDZ was present (0.5 mg/L). The microbial communities' analysis revealed that the abundance of nitrogen removal-related bacteria increased with C/N. Specifically, the abundance of ammonia-oxidizing bacteria (0.46%-0.90%) was low, and the nitrite-oxidizing bacteria (2.16%-7.13%) and denitrifying bacteria showed a significant increase (Hyphomicrobium: 0.57%-3.54%) when C/N ratio increased. The abundance of denitrifying bacterial declined by 4.82–8.56% at different C/N ratios, while nitrifying bacterial rose by 0.70–5.67%. Interestingly, the denitrifying bacteria Enterobacter, Sphingomonas and Gemmatimonas acted as mutualistic bacteria that stabilized denitrification.

Partial Nitrification Characteristics of an Immobilized Carrier in Municipal Wastewater under Low-Temperature Shock: The Role of the Nitrifying Bacterial Community Structure

To analyze the effects of the nitrifying bacterial community structure on the partial nitrification (PN) characteristics in a PN-immobilized carrier in municipal wastewater under low-temperature shock, two PN-immobilized carriers with different nitrifying bacterial communities were investigated. The E1-immobilized carrier contained a high abundance of ammonia-oxidizing bacteria (AOB; 38.59%), and the E2-immobilized carrier had a low AOB abundance of 4.78%. The results of experiments with different dissolved oxygen (DO) concentrations showed that the oxygen-limited environment inside the immobilized carrier, generated by the high AOB abundance, was critical for achieving PN. The nitrite accumulation rate (NAR) decreased from 90.0–93.9% to 84.2–88.3% for the E1-immobilized carrier and from 86.0–90.4% to 81.7–85.8% for the E2-immobilized carrier under low-temperature shock (the temperature suddenly decreased from 25 ± 1 °C to 15 ± 1 °C). The decrease in the ammonia oxidation rate due to the decreased AOB activity led to a decrease in NAR. Moreover, NOB abundance in the E2-immobilized carrier increased because of the destruction of the oxygen-limiting region in the immobilized carrier due to the low AOB abundance. Increasing the abundance of AOB in the PN-immobilized carrier could reduce the adverse effects from the low-temperature shock. The results of this study can be used to further develop immobilization technology for efficient PN in mainstream wastewater treatment.

Comparison of Biochar- and Lime-Adjusted pH Changes in N2O Emissions and Associated Microbial Communities in a Tropical Tea Plantation Soil

The use of biochar and lime (CaO) is a common approach to mitigating soil acidification. However, little is known about how biochar and lime amendments impact N2O emissions and potential microbial mechanisms. We conducted a 45-day microcosm incubation experiment to examine N2O emission and associated functional guilds to biochar and lime amendment in an acidic tea plantation soil. Results show that lime and biochar treatments significantly reduced cumulative N2O emissions by 49.69% and 63.01%, respectively, while significantly increasing cumulative CO2 emissions by 27.51% and 19.35%, respectively. Additionally, lime and biochar treatments significantly decreased the abundances of bacterial nirK, nirS, nosZ and fungal nirK genes, while increasing that of the ammonia-oxidizing bacteria (AOB) and the complete ammonia-oxidizing bacteria (comammox) amoA genes. The stimulated or inhibitory effects of biochar on functional genes abundances were higher than lime. The N2O emission rate was positively linked with the abundance of the fungal nirK gene but was negatively correlated with AOB and comammox amoA genes abundances. The random forest and linear regression analysis revealed that fungal denitrifiers were the most important predictors of N2O emissions. Lime and biochar amendments reduced the alpha diversity and altered the community composition of nirK-harboring fungal denitrifiers. Ascomycota was the dominant fungal denitrifiers belonging to the families Nectriaceae, Aspergillaceae, and Chaetomiaceae, and the relative abundances of genera Chaetomium, Penicillium and Fusarium were positively correlated with N2O emissions. Overall, our findings suggest that biochar is more effective than lime in reducing N2O emissions, and this is likely due to the powerful effects it has on community traits of nirK-harboring fungal denitrifiers.

Intercropping with BNI-sorghum benefits neighbouring maize productivity and mitigates soil nitrification and N2O emission

Sorghum (Sorghum bicolor) roots are well-known for the release of Biological Nitrification Inhibitors (BNIs), such as sorgoleone (SGLN) and methyl 3–4-hydroxyphenyl propionate (MHPP). However, the deployment of sorghums with BNIs in agriculture practices has not been widely investigated and evaluated. In this study, sorghum and maize were intercropped in field and pot cultivation to investigate the Biological Nitrification Inhibition (BNI) effect of sorghum on the productivity of both crops and soil nitrification. Inorganic N content (NO3– and NH4+), N2O emission, and the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil were analyzed. The results showed intercropping with sorghum have the potential to improve crop productivity, as indicated by the Land Equivalent Ratio greater than 1.0. Intercropping with sorghum reduced the transformation rate of NH4+ to NO3– in soils and the emission of N2O, as compared to monoculture of maize. Additionally, the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) under intercropping mode were reduced by 41% and 28% in field trials, and reduced by 59% and 23% in pot experiments, respectively. Incubation of the same soils with SGLN and/or MHPP showed that the combined treatment of both BNIs strongly inhibited nitrification and N2O emission, along with lower AOB and AOA abundances, as compared with those under the sole treatment of SGLN or MHPP. Our results indicated that the root exudates of sorghum play a significant role in inhibiting soil nitrification due to the overlapping or amplified effect of various BNIs, which contribute to the nitrogen nutrition of the neighbouring crops under intercropping mode. Therefore, intercropping with BNI crops provides an eco-friendly strategy to improve crop production with reduced N2O emission.

The single and combined effects of sulfamethazine and cadmium on soil nitrification and ammonia-oxidizing microorganisms.

The coexistence of antibiotics and heavy metals in soil has attracted increasing attention due to their negative effects on microorganisms. However, how antibiotics and heavy metals affect functional microorganisms related to nitrogen cycle remains unclear. The goals of this work were to explore the individual and combined effects of sulfamethazine (SMT) and cadmium (Cd), selected as target pollutants in soil, on potential nitrification rates (PNR) and ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) structure and diversity by 56-day cultivation experiment. Results showed that PNR in Cd- or SMT-treated soil decreased at the beginning of the experiment and then increased over time. PNR was significantly correlated with AOA and AOB-amoA relative abundance (P < 0.01). SMT addition (10 and 100mgkg-1) significantly improved AOA activity by 13.93% and 17.93%, respectively, and had no effect on AOB at day 1. Conversely, Cd at 10mgkg-1 significantly inhibited AOA and AOB by 34.34% and 37.39%, respectively. Moreover, the relative abundance of AOA and AOB in combined SMT and Cd addition clearly higher relative to single Cd at 1day. The single and combined Cd and SMT increased and reduced the community richness of AOA and AOB, respectively, but reduced the diversity of both after 56days. Cd and SMT treatments significantly changed the relative abundance of AOA phylum levels and AOB genus levels in the soil. It was mainly manifested in reducing the relative abundance of AOA Thaumarchaeota, and increasing the relative abundance of AOB Nitrosospira. Besides, AOB Nitrosospira was more tolerant to the compound addition of both than single application.

Increased N2O emission due to paddy soil drainage is regulated by carbon and nitrogen availability

Conversion from paddy field to upland cultivation, driven by economic benefits, generally increases N2O emission. However, the underlying mechanisms regarding the changes in N2O emission during the transition period of paddy soil drainage and conversion into upland remain unclear. To address this knowledge gap, a microcosm experiment was conducted to mechanistically elucidate the N2O emissions in response to paddy soil drainage and its interaction with carbon (C, glucose) and nitrogen (N, NH4Cl) availability. Results showed that N2O emissions were significantly lower in the submerged paddy soil (0.51 ± 0.03 mg N kg−1) compared to drained paddy soil (3.63 ± 0.66 mg N kg−1). The increased N2O emission was positively associated with soil NH4+ depletion and NO3− accumulation, indicating increased nitrification and NO3− supply for denitrification following paddy soil drainage. Substrate C and N availability had little effect on N2O emission from submerged paddy soil, but strongly mediated the response of N2O emission to paddy soil drainage. High C availability largely mitigated the increased N2O emission by drainage, mainly resulting from increased N2O-reductase gene (nosZ) abundance. The increased N availability interacting with drainage strongly increased N2O emissions by 1.99–16.34 folds, primarily due to increased NO3− content and gene abundances of ammonia-oxidizing bacteria (AOB) and nitrite reductase (nirKandnirS). The N2O emissions were positively correlated with the abundances of ammonia-oxidizing archaea (AOA), AOB, nirK and nirS genes, and (nirK + nirS)/nosZ ratio across treatments. Collectively, our findings suggested that the increased N2O emission due to paddy soil drainage is regulated by C and N availability, attributed to changes in NO3− content and abundances of nitrifying and denitrifying genes.

Agricultural practice negatively affects soil bacterial diversity and nitrogen functional genes comparing to adjacent native forest soils

Soil bacterial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from forest, transition, to crop soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on the bacterial 16S rRNA gene was performed for bacterial diversity and community analyses. Nitrifying and denitrifying functional genes (amoA and nirK respectively) of bacteria were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences was significantly different between crop and forest soils (p < 0.01) as well as between crop and transition soils (p = 0.01), however, there was no significant difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial relative abundance, richness, and Shannon diversity. Soil pH and nitrate contents together contributed highest to the observed different bacterial communities (Correlations = 0.381). Two operational taxonomic units (OTUs) belonging to Acidobacteriales species (OTU5, OTU8) decreased in crop soils, however, agricultural practices significantly increased an OTU of Nitrobacteraceae (OTU4). The relative abundance of ammonia-oxidizing bacteria (AOB) amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed, and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Soil pH and organic contents together contributed highest to the observed different nirK communities (Correlations = 0.443). Anthropogenic effects through agricultural practices decreased bacterial richness and Shannon diversity, increased abundance of nitrifying bacteria, and decreased diversity of denitrifying bacteria, potentially affecting the N cycling processes for healthy soils, plant productivity, and water and air quality.

Dissolved biochar fractions and solid biochar particles inhibit soil acidification induced by nitrification through different mechanisms

Biochar can inhibit soil acidification by decreasing the H+ input from nitrification and improving soil pH buffering capacity (pHBC). However, biochar is a complex material and the roles of its different components in inhibiting soil acidification induced by nitrification remain unclear. To address this knowledge gap, dissolved biochar fractions (DBC) and solid biochar particles (SBC) were separated and mixed thoroughly with an amended Ultisol. Following a urea addition, the soils were subjected to an incubation study. The results showed that both the DBC and SBC inhibited soil acidification by nitrification. The DBC inhibited soil acidification by decreasing the H+ input from nitrification, while SBC enhanced the soil pHBC. The DBC from peanut straw biochar (PBC) and rice straw biochar (RBC) decreased the H+ release by 16 % and 18 % at the end of incubation. The decrease in H+ release was attributed to the inhibition of soil nitrification and net mineralization caused by the toxicity of the phenols in DBC to soil bacteria. The abundance of ammonia-oxidizing bacteria (AOB) and total bacteria decreased by >60 % in the treatments with DBC. The opposite effects were observed in the treatments with SBC. Soil pHBC increased by 7 % and 19 % after the application of solid RBC and PBC particles, respectively. The abundance of carboxyl on the surface of SBC was mainly responsible for the increase in soil pHBC. Generally, the mixed application of DBC and SBC was more effective at inhibiting soil acidification than their individual applications. The negative impacts of dissolved biochar components on soil microorganisms need to be closely monitored.

Different responses of the gross nitrification rate to N enrichment in topsoil and subsoil

Nitrogen (N) deposition has continually increased since the industrial revolution and its rate varies widely around the world. The dynamic of soil nitrification under N enrichment affects nitrous oxide (N2O) emissions and nitrate (NO3−) leaching which are related to current environmental problems. However, the response of soil nitrification, particularly in subsoil, to a N enrichment gradient and the mechanisms involved have not been well studied. In this study, the gross nitrification rates (GNRs) and relevant abiotic and biotic factors along a N addition gradient in a field were determined at three soil depths using a 15N-labeling method. The GNR in topsoil (0–10 cm) followed a bell-shaped curve as the N addition rate increased. The GNR in subsoil (10–20 and 20–40 cm) linearly decreased as the N addition rate increased. The GNR positively correlated with the ammonia-oxidizing bacteria (AOB) abundance in topsoil (P < 0.05) and the gross mineralization rate in subsoil (P < 0.05). The results indicated that changes in the AOB abundance contributed to the bell-shaped pattern of GNR in the topsoil, and the decrease in mineralization rate contributed to the decrease in GNR with N enrichment by reducing substrate supply in the subsoil. The different responses of soil nitrification to N enrichment at different soil depths and the mechanisms involved should be taken into consideration in biogeochemical models to better predict the soil N cycling in the context of N enrichment.

Multi-scale Investigation of Ammonia-Oxidizing Microorganisms in Biofilters Used for Drinking Water Treatment.

Ammonia-oxidizing microorganisms (AOMs) include ammonia-oxidizing bacteria (AOB), archaea (AOA), and Nitrospira spp. sublineage II capable of complete ammonia oxidation (comammox). These organisms can affect water quality not only by oxidizing ammonia to nitrite (or nitrate) but also by cometabolically degrading trace organic contaminants. In this study, the abundance and composition of AOM communities were investigated in full-scale biofilters at 14 facilities across North America and in pilot-scale biofilters operated for 18 months at a full-scale water treatment plant. In general, the relative abundance of AOM in most full-scale biofilters and in the pilot-scale biofilters was as follows: AOB > comammox Nitrospira > AOA. The abundance of AOB in the pilot-scale biofilters increased with increasing influent ammonia concentration and decreasing temperature, whereas AOA and comammox Nitrospira exhibited no correlations with these parameters. The biofilters affected AOM abundance in the water passing through the filters via collecting and shedding but exhibited a minor influence on the composition of AOB and Nitrospira sublineage II communities in the filtrate. Overall, this study highlights the relative importance of AOB and comammox Nitrospira compared to AOA in biofilters and the influence of filter influent water quality on AOM in biofilters and their release into the filtrate.

Partial Substitution of Urea with Biochar Induced Improvements in Soil Enzymes Activity, Ammonia-Nitrite Oxidizers, and Nitrogen Uptake in the Double-Cropping Rice System.

Biochar is an important soil amendment that can enhance the biological properties of soil, as well as nitrogen (N) uptake and utilization in N-fertilized crops. However, few studies have characterized the effects of urea and biochar application on soil biochemical traits and its effect on paddy rice. Therefore, a field trial was conducted in the early and late seasons of 2020 in a randomized complete block design with two N levels (135 and 180 kg ha-1) and four levels of biochar (0, 10, 20, and 30 t ha-1). The treatment combinations were as follows: 135 kg N ha-1 + 0 t B ha-1 (T1), 135 kg N ha-1 + 10 t B ha-1 (T2), 135 kg N ha-1 + 20 t B ha-1 (T3), 135 kg N ha-1 + 30 t B ha-1 (T4), 180 kg N ha-1 + 0 t B ha-1 (T5), 180 kg N ha-1 + 10 t B ha-1 (T6), 180 kg N ha-1 + 20 t B ha-1 (T7) and 180 kg N ha-1 + 30 t B ha-1 (T8). The results showed that soil amended with biochar had higher soil pH, soil organic carbon content, total nitrogen content, and mineral nitrogen (NH4+-N and NO3--N) than soil that had not been amended with biochar. In both seasons, the 20 t ha-1 and 30 t ha-1 biochar treatments had the highest an average concentrations of NO3--N (10.54 mg kg-1 and 10.25 mg kg-1, respectively). In comparison to soil that had not been treated with biochar, the average activity of the enzymes urease, polyphenol oxidase, dehydrogenase, and chitinase was, respectively, 25.28%, 14.13%, 67.76%, and 22.26% greater; however, the activity of the enzyme catalase was 15.06% lower in both seasons. Application of biochar considerably increased the abundance of ammonia-oxidizing bacteria (AOB), which was 48% greater on average in biochar-amended soil than in unamended soil. However, there were no significant variations in the abundances of ammonia-oxidizing archaea (AOA) or nitrite-oxidizing bacteria (NOB) across treatments. In comparison to soil that had not been treated with biochar, the average N content was 24.46%, 20.47%, and 19.08% higher in the stem, leaves, and panicles, respectively. In general, adding biochar at a rate of 20 to 30 t ha-1 with low-dose urea (135 kg N ha-1) is a beneficial technique for improving the nutrient balance and biological processes of soil, as well as the N uptake and grain yield of rice plants.

Mainstream wastewater treatment by polyaluminium ferric chloride (PAFC) flocculation and nitritation-denitritation membrane aerated biofilm reactor (MABR)

To reduce the carbon emission of sewage treatment, a novel adsorption-biodegradation (A-B) process, flocculation pretreatment as A-stage and nitritation-denitritation MABR as B-stage, was proposed in the study. It was found that 27.37 %–49.69 % of organics can be removed from actual wastewater by flocculation with polyaluminium ferric chloride (PAFC). The pretreated wastewater could be further treated by nitritation-denitritation MABR with low aeration pressure (2–5 kPa) without any extra organics. The NH4+-N, total nitrogen (TN), and chemical oxygen demand (COD) removal efficiency can reach 100 %, 84.04 %, and 98.54 %, respectively. It was also found that the relative abundances of ammonia-oxidizing bacteria (AOB) (3.81 %–4.76 %) and denitrifying bacteria (DB) (4.30 %–5.59 %) were higher than that of nitrite-oxidizing bacteria (NOB) (2.08 %–2.39 %) in the MABR even after 130 days of operation according to the microorganism identification by 16S rRNA sequencing technology. This implied that low oxygen aeration in MABR can prevent NOB from becoming dominant bacteria. Furthermore, it was found that there were indeed traces of anaerobic ammonia oxidation (Anammox) bacteria (0.04 %–0.08 %) and were closely surrounded by other microorganisms in the MABR based on fluorescence in situ hybridization (FISH) technology. In addition, the microbial nitrogen metabolism process in the MABR was further analyzed according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). The promising mainstream A-B process proposed in this study was expected to achieve nitrogen removal with little carbon and energy consumption in wastewater treatment plants (WWTPs).

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.

Achieving stable anammox process and revealing shift of bacteria during the start-up in landfill leachate treatment.

Partial nitrification-anammox (PN/A) is an energy-efficient technology for nitrogen removal in landfill leachate treatment. Numerous studies have reported successful implementation of the PN/A process and its stable operation under laboratory conditions. One of the primary challenges in PN/A engineering applications is the mass of the seed sludge required for start-up. This study examined the PN/A using a sequence batch reactor (SBR) inoculating a common mixture to treat landfill leachate. After 70 days of operation, the system successfully realized a one-stage PN/A process and maintained a stable ammonium removal efficiency of 97.65% ± 1%, where the effluent of and nitrate ( ) were less than 4 ± 1.5 mg L-1 and 10 mg L-1 . In addition, the relative abundances of Ca. Kuenenia and Ca. Brocadia, which are typical anaerobic ammonia-oxidizing bacteria (AnAOB), increased from 0.08% to 3.99% (70 days) and 0.01% to 0.45%, respectively. The relative abundances of ammonia-oxidizing bacteria (AOB) Nitrosomonas and Nitrosospira increased from 0.9% to 2.89% and 0.007% to 0.1% (70 days), respectively. Both AnAOB and AOB are important niches of the system. PRACTITIONER POINTS: The research realized PN/A rapidly by inoculating common mixture sludge. The experiment successfully enriched AnAOB from 0.09% to 3.89% within 70 days. The article revealing the ecological roles of AOB and AnAOB in the landfill leachate treatment.

Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil

Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27–34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.

Effects of nitrogen input on soil bacterial community structure and soil nitrogen cycling in the rhizosphere soil of Lycium barbarum L.

Lycium barbarum L., goji berry, is a precious traditional Chinese medicine and it is homology of medicine and food. Its growth is heavily dependent on nitrogen. The use of chemical fertilizers has significantly promoted the yield of goji berry and the development of the L. barbarum L. industry. However, crop plants are inefficient in the acquisition and utilization of applied nitrogen, it often leads to excessive application of nitrogen fertilizers by producers, which cause negatively impact to the environment ultimately. The exploration of an interaction model which deals with crops, chemical fertilizers, and rhizosphere microbes to improve nitrogen use efficiency, is, therefore, an important research objective to achieve sustainable development of agriculture greatly. In our study, we explored the effects of nitrogen input on soil microbial community structure, soil nitrogen cycling, and the contents of nutrients in L. barbarum fruits. The structure and composition of the bacterial community in the rhizosphere soil of L. barbarum were significantly different under different nitrogen supply conditions, and high nitrogen addition inhibited the diversity and stability of bacterial communities. Low nitrogen input stimulated the relative abundance of ammonia-oxidizing bacteria (AOB), such as Nitrosospira, catalyzing the first step of the ammonia oxidation process. The results of the GLMM model showed that the level of nitrogen fertilizer (urea) input, the relative abundance of AOB, the relative abundance of Bradyrhizobium, and their combinations had significant effects on the soil nitrogen cycling and contents of nutrients in L. barbarum fruits. Therefore, we believe that moderately reducing the use of urea and other nitrogen fertilizers is more conducive to improving soil nitrogen use efficiency and Goji berry fruit quality by increasing the nitrogen cycling potential of soil microorganisms.

Reassembly of active ammonia oxidizing bacteria following invasion of exogenous microbiome in an acidic soil

Ammonia oxidation is the rate-limiting step of the global nitrogen cycle, and it is mainly catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). AOA can carry out nitrification even in acidic soils, whereas AOB activity was not consistently observed in acidic soils. In this study, we manipulated two environmental variables, i.e., the microbial composition and ammonium source (urea and ammonium sulphate), in an acidic forest soil and tested their impacts on AOB abundance, diversity and activity. Soil microcosms were established either using the native forest soil (FS) or after amending the forest soil with 5% (w/w) agricultural soil (AFS) to inoculate new, exogenous microbes. Under the same microcosm incubation condition for 28 days, AOB did not grow in FS but they grew in AFS, suggesting that exogenous microbial invasion could stimulate AOB activity in the acidic soil. Urea amendment led to higher growth of AOB than ammonium sulphate amended in AFS microcosms. DNA-based stable isotope probing revealed that the active AOB lineages were dominated by Nitrosospira cluster 3a.2 and Nitrosospira cluster 10 in the ammonium sulphate supplied soil, but shifted to co-dominance of Nitrosospira cluster 3a.2 and Nitrosospira cluster 1 after urea amendment, demonstrating differential preferences of ammonia sources of phylogenetically distinct AOB lineages. Additionally, AOB abundance showed lower stability than AOA in soils subjected to these two environmental changes, suggesting AOB are more important in determining the fate of soil nitrification following short-term environmental disturbances.

Syringic acid from rice roots inhibits soil nitrification and N2O emission under red and paddy soils but not a calcareous soil.

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N2O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N2O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N2O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH4 +) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N2O emissions. Our results support the potential for the use of the BNI SA in mitigating N2O emissions and enhancing N utilization in red and paddy soils.

Enhancement of iron-based nitrogen removal with an electric-magnetic field in an upflow microaerobic sludge reactor (UMSR).

Traditional denitrification often produces high operating costs and excessive sludge disposal expenses due to conventional carbon sources. A novel electric-magnetic field (MF) 48 mT with Fe0 and C-Fe0 powder in an upflow microaerobic sludge reactor (UMSR) improved nitrogen removal from wastewater without organic carbon resources and gave richness to the heterotrophic bacterial community. In the current study, the reactor was operated for 78 ± 2days, divided into five stages (without Fe0, with Fe0, coupling with MF, without coupling with MF, and coupling with MF again), at a hydraulic retention time (HRT) of 2.5h, with an influent loading of ammonium (NH4+-N) 50 ± 2mg/L, at 25-27°C, and less than 1.0mg/L dissolved oxygen (DO). The results demonstrated nitrogen removal efficiency enhanced after coupling with MF on the levels of NO3--N by 76% with an effluent concentration of 8.7mg/L, NH4+-N by 72% with an effluent concentration of 13.6mg/L, and total nitrogen removal (TN) by 76%, respectively. After coupling the MF with the reactor, the microbial community data analysis showed the dominant abundance of ammonia-oxidizing bacteria, heterotrophic nitrifying bacteria, and denitrifying bacteria on the level of Anaerolineaceae_uncultured 2%, which is capable of denitrification that uses Fe2+ as an electron source, Gemmatimonadaceae_uncultured 4%, Hydrogenophaga 4% which is capable of catalyzing hydrogenotrophic denitrification and correlating to nitrate removal, denitrification and desulfurization bacteria SBR1031_norank 18%, anammox-bacteria Saccharimonadales_norank 2%, and (AOM) Limnobacter 3% in the sludge.