AOA) And Bacteria Research Articles

Contrasting nitrogen dynamics across the Mid‐Atlantic Bight shelfbreak front: Insights from nitrate dual isotopes and nitrifier gene abundance

AbstractObservations and model studies suggest that front dynamics can enhance phytoplankton productivity. This study tested whether frontal systems also increase the abundance of nitrifying microbes and nitrogen recycling during repeat sampling transects across the Mid‐Atlantic Bight shelfbreak in July 2019. We measured ammonium concentrations, nitrate dual isotopes (δ15N, δ18O), and ammonia monooxygenase subunit A (amoA) genes of ammonia‐oxidizing archaea (AOA) and bacteria (AOB). In subsurface shelf waters, ammonium concentrations exceeded 2 μmol L−1, due to a temporary imbalance in regeneration from sinking particles and subsequent nitrification. The inverse correlation between nitrate δ15N values and ammonium concentrations confirmed nitrate was partially or entirely from local nitrification on the shelf. In contrast, the shelfbreak frontal zone and slope sea subsurface waters had much lower ammonium concentrations (0.1–0.2 μmol L−1) due to tight coupling between ammonium regeneration and nitrification. The deviation of nitrate δ15N and δ18O from algal uptake‐driven 1 : 1 ratio suggests concurrent nitrification in the euphotic zone. The shelfbreak front acted as an ecological boundary where AOA and AOB amoA gene numbers were partitioned, with AOAs abounding in slope waters and AOBs in shelf waters, likely due to ammonium availability. At certain slope stations, deep‐water nutrient inputs via isopycnal lifting induced by Gulf Stream intrusions caused unexpectedly high phytoplankton biomass, which doubled nitrifier abundance and potentially stimulated both ammonium regeneration and nitrification. These findings demonstrate distinct distributions of nitrifying microbes along the salinity gradient from shelf to slope and highlight the significant influence of coastal ocean‐western boundary current interactions on nitrogen biogeochemistry.

Impact of Dolomite Liming on Ammonia-Oxidizing Microbial Populations and Soil Biochemistry in Acidic Rice Paddy Soils

Background and Aims: Over the last few decades, rampant nitrogen fertilization has exacerbated soil acidification in agricultural ecosystems. To counteract this, liming has become an essential technique for rehabilitating fertility in acid-degraded agricultural soils. Our research aimed to shed light on the response of ammonia oxidizers to liming in acidic soils within a controlled rice paddy experiment. We conducted a pot experiment with rice, featuring three different treatments: a control with only soil, a low dolomite dose (LD), and a high dolomite dose (HD). Various soil properties were investigated throughout the study. Under flooding, soil pH values rose across the treatments, from 5.4 in the control to 6.8 in HD. Ammonium and nitrate levels peaked in the HD treatment, reaching 30 and 22 mg kg−1, respectively. Similarly, dissolved organic carbon and microbial biomass carbon surged at mid-season aeration, hitting highs of 101 and 30 mg kg−1, respectively, in the HD treatment. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were responsive to dolomite-lime application, with distinct reactions; AOB abundance and potential nitrification rates were positively affected by higher lime doses, whereas AOA numbers decreased over time and with dolomite application. Additionally, soil enzymes such as urease, catalase, invertase, phenol oxidase, and phosphatase also increased progressively, mirroring the rise in soil pH. This study identified increased soil pH as the critical factor influencing various soil parameters, especially the balance between AOA and AOB populations. Both AOB and AOA were sensitive to liming; AOA decreased while liming stimulated AOB abundance.

Nitrogen and phosphorus additions alter soil N transformations in a Metasequoia glyptostroboides plantation.

Nitrogen (N) and phosphorus (P) enrichment due to anthropogenic activities can significantly affect soil N transformations in forest ecosystems. However, the effects of N and P additions on nitrification and denitrification processes in Metasequoia glyptostroboides plantations, and economically important forest type in China, remain poorly understood. This study investigated the responses of soil nitrification and denitrification rates, as well as the abundances of nitrifiers and denitrifiers, to different levels of N and P additions in a 6-year nutrient addition experiment in a M. glyptostroboides plantation. Stepwise multiple regression analysis was used to identify the main predictors of nitrification and denitrification rates. The results showed that moderate N addition (N2 treatment, 2.4 mol·m-2) stimulated nitrification rates and abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), while excessive N and P additions inhibited denitrification rates and reduced the abundance of nirS-type denitrifiers. AOB abundance was the main predictor of nitrification rates under N additions, whereas microbial biomass carbon and nirS gene abundance were the key factors controlling denitrification rates. Under P additions, tree growth parameters (diameter at breast height and crown base height) and AOB abundance were the primary predictors of nitrification and denitrification rates. Our study reveals complex interactions among nutrient inputs, plant growth, soil properties, and microbial communities in regulating soil N transformations in plantation forests. This study also offers valuable insights for formulating effective nutrient management strategies to enhance the growth and health of M. glyptostroboides plantations under scenarios of increasing elevated nutrient deposition.

Impacts of Biochar and Gypsum on Ammonia-Oxidizing Microorganisms in Coastal Saline Soil

Nitrification is the core step of the soil nitrogen cycle and directly affects the nitrogen use efficiency in agricultural systems. Biochar and gypsum are two important soil amendments widely used in coastal saline farmland. However, little is known about their effects on nitrification and ammonia-oxidizing microorganisms. A one-year pot experiment with three treatments including biochar application (BC), gypsum application (SG), and no amendment (CK) was conducted, and the responses of the nitrification rate, amoA gene copies, and the diversity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to biochar and gypsum were evaluated. The results indicated that biochar and gypsum application both resulted in alterations to the soil properties. They both had inhibiting effects on nitrification and AOB amoA gene copies, whereas they had no significant effect on AOA amoA gene copies. Biochar had no significant effect on the diversity indexes of AOA, but it significantly reduced the Shannon index of AOB. Meanwhile, gypsum had no significant influence on the diversity indexes of both AOA and AOB. Biochar and gypsum did not significantly affect the community structure of AOA but did induce changes in that of AOB. In detail, biochar significantly enhanced the relative abundance of the dominant cluster Nitrosospira, whereas gypsum led to a notable increase in the relative abundance of unclassified_o_Nitrosomonadales. The Shannon index of AOB had a significant negative correlation with soil TOC, TN, and NH4+ content, and soil pH was the first primary environmental factor that affected the AOB community structure. In conclusion, biochar and gypsum inhibited nitrification by suppressing the activities of AOB and changed the diversities and community structure of AOB by altering related soil properties.

Long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol

The discovery of complete ammonia oxidizers (comammox) has dramatically altered our perception of nitrogen (N) biogeochemistry. However, their functional importance vs. the canonical ammonia oxidizers (i.e., ammonia oxidizing-archaea (AOA) and bacteria (AOB)) in agroecosystems is still poorly understood. Accordingly, a new assay using acetylene, 3,4-dimethylpyrazole phosphate (DMPP), and 1-octyne was adopted to assess the ammonia (NH3) oxidation and nitrous oxide (N2O) production activity of these functional guilds in a subtropical Inceptisol under long-term different fertilization regimes. These regimes include CK (no fertilizer control), synthetic fertilizer only (NPK), organic manure only (M) and organic manure plus synthetic fertilizer (MNPK). AOA dominated NH3 oxidation in the M treatment, while AOB dominated both NH3 oxidation and N2O production in all treatments except M. Comammox always played a minor role in both NH3 oxidation and N2O production across all treatments. Both M and MNPK treatments significantly increased the activity and growth of comammox. Compared to NPK, comammox exhibited increases of 270 % and 326 % in the NH3 oxidation rates, and increases of 1472 % and 563 % in the N2O production rates in M and MNPK, respectively. Random forest model revealed that copper (Cu), comammox abundance, and dissolved organic nitrogen (DON) were the most important predictors for the NH3 oxidation rates of comammox. Redundancy analyses (RDA) showed that fertilizer treatments significantly altered the community composition of NH3 oxidizers, and pH was the overarching parameter underpinning the community shift of the NH3 oxidizers. Overall, this study provides evidence that comammox play a minor yet unneglectable role in the nitrification of agroecosystems, and the long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol.

Biochar Combined with Garbage Enzyme Enhances Nitrogen Conservation during Sewage Sludge Composting: Evidence from Microbial Community and Enzyme Activities Related to Ammoniation

Nitrogen loss is an unavoidable problem during composting processes, and the ammonia oxidation process significantly affects nitrogen transformation. The objective of this study was to evaluate nitrogen transformation when garbage enzyme (GE), biochar (BC), pelelith (PL) and combinations thereof were added during sewage sludge composting. Meanwhile, the succession of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were also explored via quantitative polymerase chain reaction and high-throughput sequencing. The results showed that GE + BC and GE + PL treatments decreased ammonia (NH3) formation by 23.8% and 8.3%, and that of nitrous oxide (N2O) by 25.7% and 26.3% relative to the control, respectively. Simultaneously, the GE, GE + BC, and GE + PL treatments boosted the succession of AOA and AOB, and increased the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO) activities and the gene copies of AOA and AOB. The AMO activities, NH4-N, NO3-N, and C/N, significantly affect AOA and AOB community structures. The network analysis predicted that the AMO and HAO were secreted mainly by the unclassified_Archaea and norank_Crenarchaeota, whereas it also showed that the GE + BC improved microbial associations with AOA, enzymatic activity, and environmental factors. Thus, the addition of garbage enzyme and biochar appears to be a promising mitigation strategy to reduce nitrogen losses during the composting process.

The cooperative interaction of AOB and comammox clade A drives nitrification and N2O emissions in a long-term organic fertilized paddy soil

The newly discovered complete ammonia oxidizer (comammox Nitrospira) is able to single-step nitrification capability, and increased our understanding of soil nitrogen cycling. However, the response of comammox and ammonia-oxidizing bacteria (AOB) and archaea (AOA) to long-term fertilization and rhizosphere effects in paddy soils and their relative contribution to the nitrification-derived N2O emissions is still unclear. Here, we collected rhizosphere and bulk soils with thirty years of different fertilization strategies, i.e., non-fertilization (CK), chemical N, P, and K application (NPK), and NPK plus pig manure application (NPKM), respectively, to test changes in nitrification potential rate (PNR), N2O emission fluxes, abundance of ammonia oxidizers and their significant drivers. The result showed that NPKM significantly increased soil C and N levels, the proportion of soil middle-size particles (40.35–148.00 μm class), and soil PNR, but decreased soil N2O emissions, especially in the drying time of paddy (P < 0.05), compared to NPK fertilization. NPKM had the highest values of AOA, AOB, and comammox clade A amoA gene copy numbers (P < 0.05), but clade B was increased by the NPK in the rhizosphere soil. Furthermore, fertilization showed greater effects on ammonia oxidizers (except for clade B) than the rhizosphere effect. Mantel test showed that SOM, TP, pH, NH4+, and NO3− were main abiotic factors causing the niche separation among ammonia oxidizers. Linear regression analysis and structural equation model (SEM) showed that both PNR and N2O emission fluxes were significantly associated with the abundance of AOB and comammox clade A (P < 0.05). Therefore, our results underline the importance of AOB together with comammox clade A in nitrification and N2O production in long-term organic fertilized paddy fields, which could provide new ideas for the mitigation of N2O emission by adopting organic fertilization scenarios in Chinese paddy fields.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil.

Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Long-neglected contribution of nitrification to N2O emissions in the Yellow River

Rivers play a significant role in the global nitrous oxide (N2O) budget. However, the microbial sources and sinks of N2O in river systems are not well understood or quantified, resulting in the prolonged neglect of nitrification. This study investigated the isotopic signatures of N2O, thereby quantifying the microbial source of N2O production and the degree of N2O reduction in the Yellow River. Although denitrification has long been considered to be the dominant pathway of N2O production in rivers, our findings indicated that denitrification only accounted for 18.3% (8.2%–43.0%) of the total contribution to N2O production in the Yellow River, with 50.2%–80.2% being concurrently reduced. The denitrification contribution to N2O production (R2 = 0.44, p < 0.01) and N2O reduction degree (R2 = 0.70, p < 0.01) were positively related to the dissolved organic carbon (DOC) content. Similar to urban rivers and eutrophic lakes, denitrification was the primary process responsible for N2O production (43.0%) in certain reaches with high organic content (DOC = 5.29 mg/L). Nevertheless, the denitrification activity was generally constrained by the availability of electron donors (average DOC = 2.51 mg/L) throughout the Yellow River basin. Consequently, nitrification emerged as the primary contributor in the well-oxygenated Yellow River. Additionally, our findings further distinguished the respective contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to N2O emissions. Although AOB dominated the N2O production in the Yellow River, the AOA specie abundance (AOA/(AOA + AOB)) contributed up to 32.6%, which resulted in 25.6% of the total nitrifier-produced N2O, suggesting a significant occurrence of AOA in the oligotrophic Yellow River. Overall, this study provided a non-invasive approach for quantifying the microbial sources and sinks to N2O emissions, and demonstrated the substantial role of nitrification in the large oligotrophic rivers.

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

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

Deciphering the functional importance of comammox vs. canonical ammonia oxidisers in nitrification and N2O emissions in acidic agricultural soils

The discovery of comammox Nitrospira has altered our perception of the nitrogen biogeochemical cycle. However, their functional importance compared to canonical ammonia oxidisers (i.e., ammonia-oxidising bacteria (AOB) and archaea (AOA)) in agricultural soils remains elusive, especially in acidic soils. Here, we assessed the functional importance of these functional guilds in nitrification and nitrous oxide (N2O) emissions in three acidic agricultural soils by using a range of nitrification inhibitors (acetylene, 3,4-dimethylpyrazole phosphate (DMPP) and different concentrations of 1-octyne) and monitored their community assemblage and population dynamics. The sensitivity of comammox Nitrospira clade A to 1-octyne varied across soils, highlighting that the inappropriate use of 1-octyne can lead to misestimation of comammox activity. AOA were key NH3 oxidisers in the three soils, while AOB also contributed significantly to nitrification in one soil. In contrast, comammox Nitrospira always played a minor role in ammonia oxidation and N2O emissions, likely due to their low abundances, restricted cellular kinetic properties and N2O production mechanisms. Together, this study demonstrates that comammox Nitrospira play a less important role in ammonia oxidation and N2O production in acidic agricultural soils than AOA and AOB, thereby providing important novel insights into the mitigation of nitrogen fertiliser loss and N2O emissions.

Mitigating soil degradation in continuous cropping banana fields through long-term organic fertilization: Insights from soil acidification, ammonia oxidation, and microbial communities

Exploring the potential of organic fertilizers as a mitigating strategy against the negative consequences induced by prolonged use of inorganic fertilizers in high-intensity banana cultivation is critically essential. Ammonia-oxidizer are closely linked to soil acidification, and how they respond to the long term fertilized banana field soil still poorly understood. In this study, soil samples from long-term inorganic (CF), and inorganically plus organically fertilized banana fields (OF) (from 2010 to 2019) were used to investigate the soil acid buffer capacity (pHBC), the potential nitrification rate (PNR), and the community structure of bacteria, fungi, ammonia-oxidizing archaea (AOA), and bacteria (AOB). Compared to the natural soil (CK, unplanted, and unfertilized), the pH and pHBC in the long-term fertilized banana field (both CF and OF) were significantly reduced. However, the pHBC was 1.3 times higher in soil receiving OF treatment than that in CF treatment. Organic matter (OM) and total nitrogen (TN) were significantly increased in the OF treated soil, which were 1.88 and 1.6 times higher compared to the CF-treated ones. The PNR in banana soil was 3.71–4.85 times higher than in the natural soil. High-throughput sequencing results showed that Candidatus Nitrosospharea SCA1170-like AOA and Nitrosospira spp-like AOB were adapted to long-term fertilization in banana field soil. Potentially pathogenic bacteria, Xanthomonadaceae, were enriched in CF-treated soil compared to CK and OF soils. Opposingly, potentially beneficial Streptomyces and Arthrobacter were enriched in natural soil. Meanwhile, the OF-treated soil demonstrated a greater abundance of beneficial Bacillus and Alicyclobacillus. The study reveals that organic fertilizers ameliorate soil acidification, low organic matter content and microbial diversity compared to inorganic fertilizers for banana cultivation.

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.

Impacts of Climate Change and Agricultural Practices on Nitrogen Processes, Genes, and Soil Nitrous Oxide Emissions: A Quantitative Review of Meta-Analyses

Microbial-driven processes, including nitrification and denitrification closely related to soil nitrous oxide (N2O) production, are orchestrated by a network of enzymes and genes such as amoA genes from ammonia-oxidizing bacteria (AOB) and archaea (AOA), narG (nitrate reductase), nirS and nirK (nitrite reductase), and nosZ (N2O reductase). However, how climatic factors and agricultural practices could influence these genes and processes and, consequently, soil N2O emissions remain unclear. In this comprehensive review, we quantitatively assessed the effects of these factors on nitrogen processes and soil N2O emissions using mega-analysis (i.e., meta-meta-analysis). The results showed that global warming increased soil nitrification and denitrification rates, leading to an overall increase in soil N2O emissions by 159.7%. Elevated CO2 stimulated both nirK and nirS with a substantial increase in soil N2O emission by 40.6%. Nitrogen fertilization amplified NH4+-N and NO3−-N contents, promoting AOB, nirS, and nirK, and caused a 153.2% increase in soil N2O emission. The application of biochar enhanced AOA, nirS, and nosZ, ultimately reducing soil N2O emission by 15.8%. Exposure to microplastics mostly stimulated the denitrification process and increased soil N2O emissions by 140.4%. These findings provide valuable insights into the mechanistic underpinnings of nitrogen processes and the microbial regulation of soil N2O emissions.

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.

Effect of Fertigation with Struvite and Ammonium Nitrate on Substrate Microbiota and N2O Emissions in a Tomato Crop on Soilless Culture System

Struvite and ammonium nitrate (AN), as wastewater-recovered products, are possible alternatives as raw materials for nutrient solutions. However, their impact on the rhizosphere microbiota and N2O emissions is scarcely known. Therefore, the present research studies the ecological changes in the bulk-substrate microbiome and its correlation with N2O emissions in a perlite-based system tomato crop under (i) conventional synthetic fertigation management; (ii) fertigation with struvite; and (iii) struvite and AN. A high bacterial diversity and the natural presence of plant-growth-promoting rhizobacteria in a soilless system are highlighted. However, the different N-NH4+:N-NO3− ratios influence the ecological niches of ammonia-oxidizing archaea (AOA) and bacteria (AOB), with a stronger response by AOB community, while AOA kept constant regarding the fertilization applied. Despite this, enrichment of N-transforming bacterial phylotypes was relatively enhanced (mainly Nitrosomonas, Nitrosospira, and Nitrospira) concomitant with the production of N2O emissions when ammonium fertilization was overapplied. In the absence of a plant, N2O emissions were positively correlated, respectively, with Nitrosospira and AOB:AOA ratio, suggesting potential indicators for ammonium availability in the substrate. Fertilizer blends using recovered nutrients are a feasible alternative for increasing circularity in horticulture. Nevertheless, optimum fertilizer management is needed due to its influence on rhizosphere microbiota and N2O emissions.

Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.

Assessing the effectiveness of 3, 4-dimethylpyrazole phosphate (DMPP) inhibitor in mitigating N2O emissions from contrasting Cd-contaminated soils

Improving nitrogen use efficiency of chemical fertilizers is essential to mitigate the negative environmental impacts of nitrogen. Nitrification, the conversion of ammonium to nitrate via nitrite by soil microbes, is a prominent source of nitrogen loss in soil systems. The effectiveness of nitrification inhibitors in reducing nitrogen loss through inhibition of nitrification is well-documented, however, their efficacy in heavy metals-contaminated soils needs thorough investigations. The current study assessed the efficacy of nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) in reducing nitrous oxide (N2O) emissions in cadmium (Cd) contaminated paddy and red soils under lab-controlled environment. Obtained results indicated the substantial reduction in N2O emissions with DMPP in paddy and red soil by 48 and 35 %, respectively. However, Cd contamination resulted in reduced efficacy of DMPP, thus decreased the N2O emissions by 36 and 25 % in paddy and red soil, respectively. It was found that addition of DMPP had a significant effect on the abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA). Notably, the reduction in N2O emissions by DMPP varied with the abundance of AOB. Moreover, Cd pollution resulted in a significant (P < 0.05) reduction in the abundance of archaeal and bacterial amoA genes, as well as bacterial nirK, nirS, and nosZ genes. The combined treatment of Cd and DMPP had a detrimental impact on denitrifiers, thereby influencing the overall efficiency of DMPP. These findings provide novel insights into the application of DMPP to mitigate nitrification and its potential role in reducing N2O emissions in contaminated soils.

Biochar Amendment in Vermi-Wetland for Enhancing Nitrification during Excess Sludge Recycling

Vermi-wetland is a sustainable technology for recycling excess sludge in small-town areas. Although biochar (BC) amendment into the vermi-wetland could considerably boost the effectiveness of treating sludge, its impact on the nitrogen transformation in vermi-wetland remains unclear. Hence, this study aimed to explore the mechanism and performance of BC amendment into the vermi-wetland for enhancing nitrogen transformation during excess sludge recycling. The semi-aquatic plant Acorus calamus and the earthworm Eisenia fetida were planted in the designed vertical vermi-reactor, with corncob BC added to the upper and lower layers of one vermi-reactor, in comparison with the vermi-reactor without BC. The vermi-reactor with BC significantly lowered (p &lt; 0.05) ammonia nitrogen (NH4+-N) and nitrite nitrogen (NO2−-N) in the effluent by 1.63 and 4.85-fold, respectively, and increased considerably nitrate nitrogen (NO3−-N) in the effluent by 1.5-fold. The numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in the vermi-reactor with BC were greatly enriched by 6 and 1.42-fold, compared with their counterparts (p &lt; 0.05). Moreover, nirS and nirK gene copies in the vermi-reactor with BC were considerably improved (p &lt; 0.05) by 2.03 and 1.82-fold, respectively. BC significantly enhanced the growth of earthworms by 6.92-fold and promoted plant growth by 1.28-fold. In addition, the AOB members like Nitrosomonas and Nitrosospira and the AOA members like Crenarchaeota and Thaumarchaeota cohabited in BC. Overall, these results suggest that a vermi-reactor amended with BC could enhance the nitrification processes of excess sludge, thereby improving the treatment performance of vermi-wetland.

Comammox bacteria and ammonia oxidizing archaea are major drivers of nitrification in glacier forelands

This study investigated the abundance of comammox bacteria and canonical ammonia-oxidizing bacteria (AOB) and archaea (AOA), and their relative contribution to nitrification along a chronosequence of deglaciated forelands. The results showed that nitrification related gene abundance tended to increase with glacier retreat, with comammox bacteria and AOA appearing to be the most critical drivers for soil nitrification rates. These findings provide new evidence for the presence of comammox bacteria in glacier forelands and enhance our understanding of the niche differentiation of canonical nitrifier and comammox bacteria.