Exploring the efficiency of tide flow constructed wetlands for treating mariculture wastewater: A comprehensive study on antibiotic removal mechanism under salinity stress.

Antibiotic residues in aquaculture environment pose persistent threats to ecology and human health, exacerbated by salt-alkali mariculture wastewater. Yet, little is known about antibiotic removal in tidal flow constructed wetlands (TFCWs) under salinity stress, especially considering TFCW constitution, configuration, and influent water characteristics. Here, the removal performance and mechanism of different TFCWs for sulfonamide antibiotics (SAs: sulfadiazine, sulfamethazine, sulfamonomethoxine, and sulfamethoxazole) and trimethoprim (TMP) from mariculture wastewater (with low, medium, and high salinity) were evaluated alongside comparisons of environmental factors and microbial responses. Results showed substantial reduction in alkalinity (from 8.25-8.26 to 7.65-8.18), salinity (from 3.67-11.30 ppt to 3.20-10.79 ppt), and SAs concentrations (from 7.79-15.46 mg/L to 0.25-10.00 mg/L) for mariculture wastewater using TFCWs. Zeolite and yellow flag configurations exhibited superior performance in SAs removal from mariculture wastewater. Furthermore, the salt-alkali neutralization and oxygen transport capabilities of zeolite, along with the salt-alkali tolerance and biofilm formation characteristics of yellow flag, promoted the development of a biofilm in the rhizosphere dominated by oxidative stress tolerance and facultative anaerobic traits, thereby improving the TFCW microenvironment. Consequently, aerobic (Sulfuritalea and Enterobacter) and salt-tolerant (Pseudomonas) functional bacteria involved in antibiotic degradation were selectively enriched in the zeolite- and yellow flag-TFCWs, contributing to the effective biodegradation of SAs (achieving removal efficiency of 92-97 %). Besides, the high salt-alkali levels of mariculture wastewater and the strong oxygen-enriched capacity of the TFCWs not only enhanced the aerobic oxidation reaction of SAs, but also bidirectionally inhibited the substrate adsorption and anaerobic reduction process of TMP. These findings address a critical gap by investigating the efficacy of TFCWs in removing antibiotics from mariculture wastewater under various salinity conditions, providing essential insights for optimizing wetland design and improving wastewater management in mariculture environments.

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

Introduction: 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. Methods: 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. Results and Discussion: 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.

Unraveling the mechanism of interaction: accelerated phenanthrene degradation and rhizosphere biofilm/iron plaque formation influenced by phenolic root exudates.

Phenolic root exudates (PREs) secreted by wetland plants facilitate the accumulation of iron in the rhizosphere, potentially providing the essential active iron required for the generation of enzymes that degrade polycyclic aromatic hydrocarbon, thereby enhancing their biodegradation. However, the underlying mechanisms involved are yet to be elucidated. This study focuses on phenanthrene (PHE), a typical polycyclic aromatic hydrocarbon pollutant, utilizing representative PREs from wetland plants, including p-hydroxybenzoic, p-coumaric, caffeic, and ferulic acids. Using hydroponic experiments, 16S rRNA sequencing, and multiple characterization techniques, we aimed to elucidate the interaction mechanism between the accelerated degradation of PHE and the formation of rhizosphere biofilm/iron plaque influenced by PREs. Although all four types of PREs altered the biofilm composition and promoted the formation of iron plaque on the root surface, only caffeic acid, possessing a similar structure to the intermediate metabolite of PHE (catechol), could accelerate the PHE degradation rate. Caffeic acid, notable for its catechol structure, plays a significant role in enhancing PHE degradation through two main mechanisms: (a) it directly boosts PHE co-metabolism by fostering the growth of PHE-degrading bacteria, specifically Burkholderiaceae, and by facilitating the production of the key metabolic enzyme catechol 1,2-dioxygenase (C12O) and (b) it indirectly supports PHE biodegradation by promoting iron plaque formation on root surfaces, thereby enriching free iron for efficient microbial synthesis of C12O, a crucial factor in PHE decomposition.

Fate of 15N-labelled urea as affected by long-term manure substitution.

Quantifying the fate of fertilizer nitrogen (N) is essential to develop more sustainable agricultural fertilization practices. However, the fate of chemical fertilizer N, particularly in long-term manure substitution treatment regimes, is not fully understood. The present study aimed to investigate the fate of 15N-labelled urea in a chemical fertilizer treatment (CF, 240 kg 15N ha-1) and N manure 50 % substitution treatment (1/2N + M, 120 kg 15N ha-1 + 120 kg manure N ha-1) in two continuous crop seasons, based on a 10-year long-term experiment in the North China Plain (NCP). The results showed that manure substitution greatly enhanced 15N use efficiency (15NUE) (39.9 % vs. 31.3 %) and suppressed 15N loss (6.9 % vs. 7.5 %) compared with the CF treatment in the first crop. However, the N2O emissions factor in the 1/2N + M treatment was increased by 0.1 % (0.5 kg 15N ha-1 for CF vs. 0.4 kg 15N ha-1 for 1/2N + M) compared with the CF treatment, although N leaching and NH3 volatilization rates decreased by 0.2 % (10.8 kg 15N ha-1 for CF vs. 5.1 kg 15N ha-1 for 1/2N + M) and 0.5 % (6.6 kg 15N ha-1 for CF vs. 2.8 kg 15N ha-1 for 1/2N + M), respectively. In which, only NH3 volatilization presented significantly difference between treatments. It is important to note that in the second crop, the residual 15N in soil (0-20 cm) remained mostly in the soil for the CF (79.1 %) and the 1/2N + M treatment (85.3 %), and contributed less to crop N uptake (3.3 % vs. 0.8 %) and leached losses (2.2 % vs. 0.6 %). This proved that manure substitution could enhance the stabilization of chemical N. These results suggested that long-term manure substitution effectively increases NUE, suppresses N loss, and improves N stabilization in soil, but negative impacts such as N2O emissions due to climate change should be investigated further.

Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils.

The objectives of this study were to investigate the abundance and community composition of comammox Nitrospira under: (i) pasture-based dairy farms from different regions, and (ii) different land uses from the same region and soil type. The results clearly showed that comammox Nitrospira were most abundant (3.0 × 106 copies) under the west coast dairy farm conditions, where they were also significantly more abundant than canonical ammonia oxidisers. This was also true in the Canterbury dairy farm. The six land uses investigated were pine monoculture, a long term no input ecological trial, sheep + beef and Dairy, both irrigated and non-irrigated. It was concluded that comammox Nitrospira was most abundant under the irrigated dairy farm (2.7 × 106 copies). Contrary to the current industry opinion, the relatively high abundance of comammox Nitrospira under fertile irrigated dairy land suggests that comammox Nitrospira found in terrestrial ecosystems may be copiotrophic. it was also determined that comammox Nitrospira was more abundant under irrigated land use than their non-irrigated counterparts, suggesting that soil moisture is a key environmental parameter influencing comammox abundance. Comammox abundance was also positively correlated with annual rainfall, further supporting this theory. Phylogenetic analysis of the comammox Nitrospira detected determined that 17 % of the comammox community belonged to a newly distinguished subclade, clade B.2. The remaining 83 % belonged to clade B.1. No sequences from clade A were found.

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha-1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.

In situ nitrous oxide and dinitrogen fluxes from a grazed pasture soil following cow urine application at two nitrogen rates.

Cattle grazing of pastures deposits urine onto the pasture soil at high nitrogen (N) rates that exceed the pasture's immediate N demands, increasing the risk of N loss. Nitrous oxide (N2O), a greenhouse gas, and dinitrogen (N2) are lost from the cattle urine patches. There is limited information on the in situ loss of N2 from grazed-pasture systems which is needed for understanding pasture soil N dynamics and balances. The 15N flux method was used to determine N2 and N2O fluxes over time following synthetic urine-15N application at either 400 or 800 kg N ha-1 to a grazed perennial pasture soil. Results showed that daily N2O fluxes were higher under 800 kg N ha-1 than under 400 kg N ha-1, but there was no significant difference in N2 fluxes. Cumulative N2O emissions from soil with 400 kg N ha-1 and 800 kg N ha-1 applied represented 0.16 ± 0.08% and 0.43 ± 0.08% of deposited N, respectively, while emitted N2 accounted for 32.1 ± 4.1% and 14.4 ± 1.7%, respectively, over 95 days after urine application. Codenitrification and denitrification co-occurred, with denitrification accounting for 97.9 to 98.5% of total N2 production. Recovery of urine-15N in pasture decreased with increasing N rate with 14.7 ± 0.5% and 9.9 ± 0.8% recovered at 400 and 800 kg N ha-1, respectively after 95 days. The N2O/(N2 + N2O) product ratio was generally higher during periods of nitrification of urine-N (the first month after urine application) but with no clear relationship to other measured variables. Contrary to our hypothesis, an elevated urine-N rate did not enhance N2 loss. This is speculated to be due to enhanced ammonia volatilisation and transfer of N as nitrate, to deeper soil layers. Soil relative gas diffusivity indicated that high N2 fluxes resulted from entrapped N2 diffusing from the draining soil.

A Genomic Analysis of Bacillus megaterium HT517 Reveals the Genetic Basis of Its Abilities to Promote Growth and Control Disease in Greenhouse Tomato.

Bacillus megaterium is well known as a plant growth-promoting rhizobacterium, but the relevant molecular mechanisms remain unclear. This study aimed to elucidate the effects of B. megaterium HT517 on the growth and development of and the control of disease in greenhouse tomato and its mechanism of action. A pot experiment was conducted to determine the effect of B. megaterium on tomato growth, and this experiment included the HT517 group (3.2 × 108 cfu/pot) and the control group (inoculated with the same amount of sterilized suspension). An antagonistic experiment and a plate confrontation experiment were conducted to study the antagonistic effect of B. megaterium and Fusarium oxysporum f.sp. lycopersici. Liquid chromatography-mass spectrometry was used to determine the metabolite composition and metabolic pathway of HT517. PacBio+Illumina HiSeq sequencing was utilized for map sequencing of the samples. An in-depth analysis of the functional genes related to the secretion of these substances by functional bacteria was conducted. HT517 could secrete organic acids that solubilize phosphorus, promote root growth, secrete auxin, which that promotes early flowering and fruiting, and alkaloids, which control disease, and reduce the incidence of crown rot by 51.0%. The complete genome sequence indicated that the strain comprised one circular chromosome with a length of 5,510,339 bp (including four plasmids in the genome), and the GC content accounted for 37.95%. Seven genes (pyk, aceB, pyc, ackA, gltA, buk, and aroK) related to phosphate solubilization, five genes (trpA, trpB, trpS, TDO2, and idi) related to growth promotion, eight genes (hpaB, pheS, pheT, ileS, pepA, iucD, paaG, and kamA) related to disease control, and one gene cluster of synthetic surfactin were identified in this research. The identification of molecular biological mechanisms for extracellular secretion by the HT517 strain clarified that its organic acids solubilized phosphorus, that auxin promoted growth, and that alkaloids controlled tomato diseases.

Attenuation of antibiotic resistance genes in livestock manure through vermicomposting via Protaetia brevitarsis and its fate in a soil-vegetable system.

Scarab larvae (Protaetia brevitarsis) could transform large quantities of agricultural waste into compost, providing a promising bio-fertilizer for soil management. There is an urgent need to assess the risk of antibiotic resistance genes (ARGs) in soil-vegetable system with application of compost derived from P. brevitarsis larvae. We conducted a pot experiment to compare the changes of ARGs in the soil and lettuce by adding four types of manure, livestock manure (chicken and swine manure) and the corresponding larval frass. Significantly low numbers of ARGs and mobile genetic elements (MGEs) were detected in both larval frass compared with the corresponding livestock manure. Pot experiment showed that the detected numbers of ARGs and MGEs in bulk soil, rhizosphere soil, and root endophytes were significantly lower in the frass-amended treatments than the raw manure-amended treatments. Furthermore, the relative abundance of ARGs and MGEs with application of chicken-frass was significant lower in rhizosphere soil and leaf endophyte. Using non-metric multidimensional scaling analysis, the patterns of soil ARGs and MGEs with chicken-frass application were more close to those from the bulk soil in the control. Structural equation models indicated that livestock manure addition was the main driver shaping soil ARGs with raw manure application, while MGEs were the key drivers in frass-amended treatments. These findings demonstrated that application of livestock manure vermicomposting via scarab larvae (P. brevitarsis) may be at low risk in spreading manure-borne ARGs through soil-plant system, providing an alternative technique for reducing ARGs in organic waste.

Corn cobs efficiently reduced ammonia volatilization and improved nutrient value of stored dairy effluents.

Dairy farms produce considerable quantities of nutrient-rich effluent, which is generally stored before use as a soil amendment. Unfortunately, a portion of the dairy effluent N can be lost through volatilization during open pond storage to the atmosphere. Adding of covering materials to effluent during storage could increase contact with NH4+ and modify effluent pH, thereby reducing NH3 volatilization and retaining the effluent N as fertilizer for crop application. Here the mitigation effect of cover materials on ammonia (NH3) volatilization from open stored effluents was measured. A pilot-scale study was conducted using effluent collected at the Youran Dairy Farm Company Limited, Luhe County, Jiangsu, China, from 15 June to 15 August 2019. The study included seven treatments: control without amendment (Control), 30-mm × 25-mm corn cob pieces (CC), light expanded clay aggregate - LECA (CP), lactic acid (LA) and lactic acid plus CC (CCL), CP (CPL) or 20-mm plastic balls (PBL). The NH3 emission from the Control treatment was 120.1 g N m-2, which was increased by 38.1% in the CP treatment, possibly due to increased effluent pH. The application of CC reduced NH3 loss by 69.2%, compared with the Control, possibly due to high physical resistance, adsorption of NH4+ and effluent pH reduction. The lactic acid amendment alone and in combination with other materials also reduced NH3 volatilization by 27.4% and 31.0-46.7%, respectively. After 62 days of storage, effluent N conserved in the CC and CCL treatments were 21.0% and 22.0% higher than that in the Control (P < 0.05). Our results suggest that application of corn cob pieces, alone or in combination with lactic acid, as effluent cover could effectively mitigate NH3 volatilization and retain N, thereby enhancing the fertilizer value of the stored dairy effluent and co-applied as a soil amendment after two months open storage.

Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China.

Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.

Nitrous oxide emissions from China's croplands based on regional and crop-specific emission factors deviate from IPCC 2006 estimates.

Calculated N2O emission factors (EFs) of applied nitrogen (N) fertilizer are currently based upon a single, universal value advocated by the IPCC (Inter-governmental Panel on Climate Change) even though EFs are thought to vary with climate and soil types. Here, we compiled and analyzed 151 N2O EF values from agricultural fields across China. The EF of synthetic N applied to these croplands was 0.60%, on average, but differed significantly among six climatic zones across the country, with the highest EF found in the north subtropical zone for upland fields (0.93%) and the lowest in the middle subtropical zone for paddy fields (0.20%). Precipitation and soil pH, which showed non-linear relationships with EF, are among the factors governing it, explaining 7.0% and 8.0% of the regional variation in EFs, respectively. Annual precipitation was the key factor regulating N2O emissions from synthetic N fertilizers. Among crop types, legume crops had the highest EFs, which were significantly (P < 0.05) higher than those of cereals. Total soil N2O emissions from fertilized croplands with maize, rice, wheat, and vegetables in China, calculated using the climatic zone (regional) EFs, were estimated to be 239 Gg N yr-1 with an uncertainty of 21%. Importantly, this value was substantially (33%) lower than that (357 Gg N yr-1) derived from the IPCC default EF but close to the 253 Gg N yr-1 estimated using crop-specific EFs. N2O emissions from applied synthetic N fertilizer accounted for 66.5% of the total annual N2O emissions from China's maize, rice, wheat and vegetable fields. Taken together, our study's results strongly suggest that regional EFs should be included for accurate N2O inventories from croplands across China.

Differentiated Mechanisms of Biochar Mitigating Straw-Induced Greenhouse Gas Emissions in Two Contrasting Paddy Soils.

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH4 and N2O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH4 and N2O emissions. However, little is known about their interactive effect on CH4 and N2O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH4 and N2O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH4 emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH4 emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N2O emissions at low input rate (S1) but significantly increased N2O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N2O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH4 and N2O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Assessing the Impact of Non-Urea Ruminant Urine Nitrogen Compounds on Urine Patch Nitrous Oxide Emissions.

Urea, the dominant form of N in ruminant urine, degrades in soil to produce NO emissions. However, the fate of non-urea urine N compounds (NUNCs) in soil and their contribution to urine patch NO emissions remain unclear. This study evaluated five NUNCs: allantoin (10%), creatinine (3%), creatine (3%), uric acid (1%), and (hypo)xanthine (0.6%), where numbers in parentheses represent the average percentage of total urine N. The fates of NUNCs in a pasture soil were determined using N-labeled NUNCs in a laboratory trial. Two NUNCs, hypoxanthine and creatine, were added to the soil with perennial ryegrass ( L.) present and sampled over time for soil inorganic N, NO emissions, and plant N dynamics. The N enrichments of soil inorganic N and plant N were significantly increased within 24 h of NUNC application, indicating rapid microbial degradation and plant uptake of NUNCs in pasture soil. An autumn field trial was also conducted to evaluate the in situ impact of varying concentrations of NUNCs on urine patch NO emissions. Increasing the proportion of urine N excreted as NUNCs did not alter the urine patch NO emission factor, soil inorganic N concentrations, or plant N uptake. It is concluded that NUNCs rapidly degrade in pasture soil and that an increased ruminant excretion of urine N as NUNCs does not significantly alter the urine patch NO emission factor.

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization.

Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.

The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand.

An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg-1), Zn (20 and 50 mg kg-1), and Cd (2 and 10 mg kg-1) were incubated for 14 days and then treated with 500 mg kg-1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.

Confirmation of co-denitrification in grazed grassland.

Pasture-based livestock systems are often associated with losses of reactive forms of nitrogen (N) to the environment. Research has focused on losses to air and water due to the health, economic and environmental impacts of reactive N. Di-nitrogen (N2) emissions are still poorly characterized, both in terms of the processes involved and their magnitude, due to financial and methodological constraints. Relatively few studies have focused on quantifying N2 losses in vivo and fewer still have examined the relative contribution of the different N2 emission processes, particularly in grazed pastures. We used a combination of a high (15)N isotopic enrichment of applied N with a high precision of determination of (15)N isotopic enrichment by isotope-ratio mass spectrometry to measure N2 emissions in the field. We report that 55.8 g N m(-2) (95%, CI 38 to 77 g m(-2)) was emitted as N2 by the process of co-denitrification in pastoral soils over 123 days following urine deposition (100 g N m(-2)), compared to only 1.1 g N m(-2) (0.4 to 2.8 g m(-2)) from denitrification. This study provides strong evidence for co-denitrification as a major N2 production pathway, which has significant implications for understanding the N budgets of pastoral ecosystems.

Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on methanotroph abundance and methane uptake in a grazed pasture soil.

Methane-oxidizing bacteria (methanotrophs) in the soil are a unique group of methylotrophic bacteria that utilize methane (CH4) as their sole source of carbon and energy which limit the flux of methane to the atmosphere from soils and consume atmospheric methane. A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of methanotrophs and on methane flux in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied at 10 kg ha(-1). The results showed that both the DNA and selected mRNA copy numbers of the methanotroph pmoA gene were not affected by the application of urea, urine or DCD. The methanotroph DNA and mRNA pmoA gene copy numbers were low in this soil, below 7.13 × 10(3) g(-1) soil and 3.75 × 10(3) µg(-1) RNA, respectively. Daily CH4 flux varied slightly among different treatments during the experimental period, ranging from -12.89 g CH4 ha(-1) day(-1) to -0.83 g CH4 ha(-1) day(-1), but no significant treatment effect was found. This study suggests that the application of urea fertilizer, animal urine returns and the use of the nitrification inhibitor DCD do not significantly affect soil methanotroph abundance or daily CH4 fluxes in grazed grassland soils.

Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on ammonia oxidizers and N2O emissions in a grazed pasture soil.

Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) are important drivers of a key step of the nitrogen cycle - nitrification, which affects the production of the potent greenhouse gas, nitrous oxide (N2O). A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of AOB and AOA and on N2O emissions in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied to some of the N treatments at 10 kg ha(-1). The results showed that the AOB amoA gene copy numbers were greater than those of AOA. The highest ratio of the AOB to AOA amoA gene copy numbers was 106.6 which occurred in the urine-N 600 treatment. The AOB amoA gene copy numbers increased with increasing nitrogen application rates. DCD had a significant impact in reducing the AOB amoA gene copy numbers especially in the high nitrogen application rates. N2O emissions increased with the N application rates. DCD had the most significant effect in reducing the daily and total N2O emissions in the highest nitrogen application rate. The greatest reduction of total N2O emissions by DCD was 69% in the urine-N 600 treatment. The reduction in the N2O emission factor by DCD ranged from 58% to 83%. The N2O flux and NO3(-)-N concentrations were significantly correlated to the growth of AOB, rather than AOA. This study confirms the importance of AOB in nitrification and the effect of DCD in inhibiting AOB growth and in decreasing N2O emissions in grazed pasture soils under field conditions.

A review of ammonia-oxidizing bacteria and archaea in Chinese soils.

Ammonia (NH(3)) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N(2)O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.