Potential Nitrification Research Articles

Assessment of the risks of N–loss to groundwater from data on N–balance surplus in Spanish crops: An empirical basis to identify Nitrate Vulnerable Zones

The aim of this research was to conduct an empirical assessment of the risks of N–loss to groundwater associated with land use (LU), based on annual data on the net N–balance surplus in Spanish crops. These data were used to generate a detailed risk rating system reflecting the potential risks of N–loss from agriculture. The new LU ratings were used to assess the specific vulnerability of groundwater to nitrate pollution, by using the LU–IV procedure (Arauzo 2017).The study area included the catchment areas of 12 alluvial aquifers associated to tributaries of the Ebro River (Spain). Most of the alluvial aquifers were chronically polluted by nitrate, with only a few remaining unaffected by pollution. The LU maps from two different base maps (MCAE 2000–09; SIOSE 2011) were used to generate the respective versions of the map of vulnerability to nitrate pollution using the LU–IV procedure. Potential nitrate vulnerable zones (NVZ) were extracted from different models of vulnerability for comparison with the map of groundwater nitrate content. The models compared were the following: model A (LU–IV procedure, based on MCAE 2000–09 and using LU ratings from N–surpluses in Spanish crops), model B (LU–IV procedure, based on SIOSE 2011 and using LU ratings from N–surpluses in Spanish crops), model C (LU–IV procedure, based on MCAE 2000–09 and using LU ratings from bibliographical references; Arauzo, 2017), model D (IV index), model E (DRASTIC index), and model F (GOD index).Results confirmed, as expected, that models A and B proved to be the best risk predictors, both for polluted groundwater areas and for areas at risk of being polluted. These results support the high level of reliability of the LU–IV procedure, when applying the LU ratings obtained empirically from the N–surpluses.

Effect of C/N ratio variations on Muara Karang sediment in oxidizing high concentrated ammonia and identification of nitrifying bacteria using VITEK 2

Oxidation of ammonia in the environment is known as nitrification. The process itself is a two-step process which oxidizes ammonia into nitrite then nitrate. A research was conducted to study the effect of C/N ratio variations in oxidizing high concentrated ammonia (100 ppm) by the bacteria isolated from the sediments collected from Muara Karang. The variations of C/N ratio implemented in the systems were 5:1, 10:1, 15:1, and 20:1 with glucose as the carbon source and ammonium sulphate as the nitrogen source. Parameters measured during the research were ammonia and nitrate concentrations. Identification of bacteria from the sediments was performed using VITEK 2 identification kits. The results revealed a significant difference (α=0.05) in ammonia concentrations between treated groups, whilst no differences were noted in nitrate (α=0.001) concentrations. Potential nitrification bacteria from the systems were identified as Acinetobacter ursingii (88%), Pseudomonas aeruginosa (99%), and Shewanellaputrefaciens (91%.)

Inhibitory Effects of Different Types and Doses of Herbicides on Soil Nitrification Potentials

To elucidate the inhibitory effects of different herbicides on soil nitrification, eight widely used herbicides, i.e., acetochlor, atrazine, dicamba, isoproturon, paraquat, puma, tribenuron-methyl, and 2,4-dichlorophenoxyacetic acid butyl ester (2,4-Dbe), which represent different chemical taxonomy were selected. Our results indicated that herbicide 2,4-Dbe displayed the best inhibitory effect on nitrification, followed by puma and tribenuron-methyl, whereas the remaining five herbicides exhibited less effect when 10 mg of active ingredient (A.I.) of every herbicide per kg of soil was applied in vegetable-planting soil. The inhibition appeared when 5–100 mg of A.I. 2,4-Dbe was employed, which was enhanced with an increment in its dose in both vegetable-planting and fluvo-aquic soils. However, the inhibitory effect of 10 mg of A. I. 2,4-Dbe exhibited obvious differences in these two types of soils, where the duration of inhibition was shorter as it only continued about a week in fluvo-aquic and calcic cambisols soils with strong nitrification activity but poorer effect as compared to 10 mg of dicyandiamide (DCD). In contrast, the duration of inhibition exceeded 2 months in dryland red and shajiang black soils with a weak nitrification activity which was equivalent to DCD. In addition, comparing with five nitrification inhibitors, 10 mg of 2,4-Dbe had better inhibition than the substituted pyrimidine (AM) and sulfocarbamide (SU), but was equivalent to DCD, nitrapirin, and 3,4-dimethylpyrazole phosphate (DMPP) at their recommended application rates in dryland red soil. These obtained data clearly indicated that 2,4-Dbe could play a stronger role as a nitrification inhibitor in soils.

Genetic variation in tree leaf chemistry predicts the abundance and activity of autotrophic soil microorganisms

AbstractGenetic variation in the chemistry of plant leaves can have ecosystem‐level consequences. Here, we address the hypothesis that genetic variation in foliar condensed tannins along a Populus hybridization gradient influences soil ammonia oxidizers, a group of autotrophic microorganisms that perform the first step of nitrification and are not dependent on carbon derived from plant photosynthesis. Evidence that genetically based plant traits influence the abundance and activity of autotrophic soil microbes would greatly expand the concept of extended plant phenotypes. We found that increasing foliar condensed tannin concentration reduced rates of soil nitrification potential by ~75%, reduced the abundance of ammonia‐oxidizing archaea by ~66%, but had no effect on ammonia‐oxidizing bacteria. Other indices that often drive nitrification rates, including soil total nitrogen, foliar nitrogen, and soil pH, were not significant predictors of either the activity or the abundance of ammonia oxidizers, suggesting genetic variation in foliar condensed tannins may be the dominant regulating factor. These results demonstrate the condensed tannin phenotypes of two different tree species and their naturally occurring hybrids have extended effects on a key ecosystem process and provide evidence for indirect genetic linkages among autotrophs across at least two domains of life.

Reduction of N2O emission by biochar and/or 3,4-dimethylpyrazole phosphate (DMPP) is closely linked to soil ammonia oxidizing bacteria and nosZI-N2O reducer populations

Biochar has been demonstrated to reduce nitrous oxide (N2O) emissions from soils, but its effect is highly soil-dependent. In particular, in soils with strong nitrification potential, biochar addition may increase N2O emissions. Thus, in soils with strong nitrification potential, the combination of biochar with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) may be more effective in reducing N2O emissions than biochar alone. However, the combined use of biochar and DMPP on soil N2O emissions is relatively unexplored, and underlying microbial mechanisms of how biochar and/or DMPP amendment affect N2O emissions is still largely unknown. Here, a 30-day incubation experiment was established with four treatments: CK (control), BC (biochar), DMPP, and BD (biochar and DMPP), all at agronomically recommended rates, and N cycling assessed following addition of urea. Treatment of soil with BC, DMPP and BD reduced N2O emissions (compared with urea alone) by 59.1%, 95.5% and 74.1%, respectively. Quantification of N cycling genes (amoA, nirS, nirK, and nosZ) indicated that biochar stimulated growth of ammonia oxidizing archaea (AOA) and bacteria (AOB), while DMPP alone inhibited the activity and growth of AOB. In the BD treatment, DMPP was absorbed onto biochar reducing its efficacy in inhibiting AOB growth. The response patterns of nirS/nirK nitrite-reducing denitrifiers to biochar and/or DMPP addition varied among clades. Notably, biochar and/or DMPP increased the abundance of nosZI and nosZII-N2O reducers, but nosZI-clade taxa were more closely associated with reducing N2O emission than nosZII taxa. Overall, our findings proved that the dynamics of AOB and nosZI-N2O reducers resulting from the addition of biochar and/or DMPP played a key role in governing soil N2O emissions.

Efficacy of aucubin as a nitrification inhibitor assessed in two Canterbury field trials

ABSTRACTRuminant urine patches are nitrous oxide (N2O) emission hot-spots and compounds that inhibit nitrification in urine-affected soils, a key step in soil N2O production, can significantly reduce N2O emissions. Aucubin, a potential nitrification inhibitor found in plantain (Plantago lanceolata) was assessed in two field trials for its efficacy in reducing urine patch nitrate (NO3−) accumulation and N2O emissions. Plantain leaf extract or commercially derived pure aucubin was added to urine, alongside a control and urine only treatment, and applied to standard gas chambers and monitored for 35 days. While there were some daily differences between treatment soil nitrogen and N2O emissions, there were no overall significant differences between cumulative N2O emissions. Aucubin, applied as a one-off dose, seems to act as a nitrification inhibitor for a short period after application onto soil, but it’s inhibitory effects are not sufficient to produce significant reductions in overall urine patch N2O emissions.

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake.

Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study, using RNA-based real-time quantification and clone library analysis, demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse in high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake regions.

Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes.

Nitrogen (N) fertilization in agricultural soils has been receiving worldwide attention due to its detrimental effects on ecosystem services, particularly on microbial N transformation. However, few studies provide a complete picture of N-fertilization effects on the N transformation cycle within a single agricultural ecosystem. Here, we explored the main steps of the microbial N cycle, using targeted gene abundances as proxies, in relation to soil properties, following 35 years of N-fertilization at increasing rates (0, 202 and 269 kg N/ha) in continuous corn (Zea mays L.) and corn-soybean [Glycine max (L.) Merr.] rotations. We used real-time quantitative polymerase chain reaction (qPCR) for the quantification of phylogenetic groups and functional gene screening of the soil microbial communities, including genes encoding critical enzymes of the microbial N cycle: nifH (N2 fixation), amoA (first step of nitrification), nirK and nirS (first step of denitrification), and nosZ (last step of denitrification). Our results showed that long term N-fertilization increased the abundance of fungal communities likely related to decreases in pH, and an enrichment of Al3+ and Fe3+ in exchange sites at the expense of critical macro and micronutrients. At the same time, long term N-fertilization damaged potential biological N2 fixation by significantly reducing the abundance of nifH genes in both continuous and rotated corn systems, while accelerating potential nitrification activities under continuous corn by increasing the abundance of bacterial amoA. Fertilization did not affect the abundance of denitrifying groups. Altogether, these results suggest that N fertilization in corn crops potentially decreases N2 acquisition by free-living soil microbes and stimulates nitrification activities, thus creating a vicious loop that makes the overall agricultural system even more dependent on external N inputs.

Earthworms Mitigate Pesticide Effects on Soil Microbial Activities.

Earthworms act synergistically with microorganisms in soils. They are ecosystem engineers involved in soil organic matter degradation and nutrient cycling, leading to the modulation of resource availability for all soil organisms. Using a soil microcosm approach, we aimed to assess the influence of the earthworm Aporrectodea caliginosa on the response of soil microbial activities against two fungicides, i.e., Cuprafor Micro® (copper oxychloride, a metal) and Swing® Gold (epoxiconazole and dimoxystrobin, synthetic organic compounds). The potential nitrification activity (PNA) and soil enzyme activities (glucosidase, phosphatase, arylamidase, and urease) involved in biogeochemical cycling were measured at the end of the incubation period, together with earthworm biomass. Two common indices of the soil biochemistry were used to aggregate the response of the soil microbial functioning: the geometric mean (Gmean) and the Soil Quality Index (SQI). At the end of the experiment, the earthworm biomass was not impacted by the fungicide treatments. Overall, in the earthworm-free soil microcosms, the two fungicides significantly increased several soil enzyme and nitrification activities, leading to a higher GMean index as compared to the non-treated control soils. The microbial activity responses depended on the type of activity (nitrification was the most sensitive one), on the fungicide (Swing® Gold or Cuprafor Micro®), and on the doses. The SQI indices revealed higher effects of both fungicides on the soil microbial activity in the absence of earthworms. The presence of earthworms enhanced all soil microbial activities in both the control and fungicide-contaminated soils. Moreover, the magnitude of the fungicide impact, integrated through the SQI index, was mitigated by the presence of earthworms, conferring a higher stability of microbial functional diversity. Our results highlight the importance of biotic interactions in the response of indicators of soil functioning (i.e., microbial activity) to pesticides.

Irrigation and Nitrogen Fertilizer Rate Impacts on Soil Nitrate in Potato Production

ABSTRACTParts of the Kern County have high nitrate levels in groundwater. A State Water Resources Control Board commissioned report has indicated that crop land agriculture is the main source of nitrates in the groundwater. Annual rainfall is less than 20 cm, thus irrigation is necessary for optimum crop production. A project was undertaken to evaluate current nitrogen fertility and irrigation scheduling in potato production and their contribution, or lack thereof, to nitrate movement in the soil profile and potential nitrate contamination of groundwater. A line-source sprinkler plot area was established to create soil moisture regimes of 120% of target, target (optimum soil moisture for potato growth) and 80% of target. Pre-plant and post-harvest soil samples were collected to a depth of 2 meters. Plant, root and tuber samples were collected and analyzed for nitrogen content. Soil moisture and irrigation amounts were monitored. Plant dry matter and tuber yield increased with each N rate increase. The high N rate increased plant growth disproportionally to the increased tuber yield. Appropriate irrigation scheduling did not produce water movement beyond the effective potato rooting zone. Excessive irrigation moved soil nitrate deeper into the soil profile.

Effects of chitin and temperature on sub-Arctic soil microbial and fungal communities and biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4-dinitrotoluene (DNT).

Climate warming in the Arctic and the thawing of frozen carbon stocks are leading to uncertainty as to how bacterial communities will respond, including pollutant degrading bacteria. This study investigated the effects of carbon stimulation and temperature on soil microbial community diversity and explosive biodegradation in two sub-Arctic soils. Chitin as a labile carbon source stimulated overall microbial activities as reflected by increases in basal respiration (three to tenfold) and potential nitrification activity (two to fourfold) compared to unamended soil. This stimulation extended to 2,4-dinitroluene- (DNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-degrading microorganisms either directly or via co-metabolic reaction mechanisms. A stimulatory effect of the incubation temperature (2, 12, or 22°C) on these microbial activities was also observed, but the chitin stimulation caused greater shifts in the structure of the bacterial and fungal communities. The first reported occurrence of an associated role of chitinolytic bacteria belonging to Cellulomonadaceae and chitinolytic fungi belonging to Mortierellaceae in explosive biodegradation is described. This study found that sub-Arctic soil microbial communities were adapted to respond quickly to an increase in labile carbon sources over the range of temperatures used in this study. The warming climate in the Arctic could benefit explosive contaminated soil clean-up by providing non-recalcitrant carbon sources that stimulate overall microbial activity and correspondingly explosive biodegradation.

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems

Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.

Hierarchical drivers of soil microbial community structure variability in \u201cMonte Perdido\u201d Massif (Central Pyrenees)

Microbial activity is highly dependent on climatic factors (moisture and temperature) and edaphic characteristics in temperate ecosystems. Moreover, soil microbial community composition in high mountain areas is less known when compared to plant communities. In this study we investigated the soil microbial community from a functional perspective using PLFA (phospholipid fatty acid) methods in the four aspects of four summits (2,242 – 3,012 m above sea level) in the Spanish Central Pyrenees. Soil organic carbon (C), microbial biomass and nutrient dynamics (N{H}_{4}^{+} + N{O}_{3}^{-}, N mineralization and nitrification potential) were also determined. Microbial biomass C was highest in the lowermost summit and decreased by approximately 50, 14 and 12% with increasing altitude. In each summit soil N{H}_{4}^{+} and N{O}_{3}^{-} concentrations differed significantly among summits and aspects. Soil nitrification potential varied significantly between the factors summit and aspects, e.g., southerly vs. northerly, easterly vs. westerly aspects. Gram negative bacteria and Actinobacteria functional groups dominated the microbial community, with almost 40% of the total PLFA. Non-metric multidimensional scale (NMS) analysis showed that most of the PLFA functional groups were present in all summits and aspects, although with specific biomarkers. A high abundance of biomarkers 16:1ω9c and 16:0 2OH (gram negative bacteria) were obtained in the lowermost summit, while the biomarkers 16.1ω7cDMA (anaerobes) and 19:3ω6c (Eukaryote) were only found in the uppermost summit. Linear mixed model (lmm) analysis was used with summit as fixed effect and aspect as random effect. In general, our results demonstrate a fundamental role for environment, principally moisture, temperature and organic matter in explaining the pattern observed for soil PLFA biomarkers. Under a global change scenario, we need to shed light on the relationships between soil microbial functional groups and soil nutrient-related variables in order to identify the associated patterns of decomposition rates and soil processes driven by microbial communities in mountain areas. The results could thus be used in global predictive models on climate change impact on C or N cycles in these environments.

Connectivity and Nitrate Uptake Potential of Intermittent Streams in the Northeast USA

Non-perennial streams dominate the extent of stream networks worldwide. Intermittent streams can provide ecosystem services to the entire network – including nitrate uptake to alleviate eutrophication of coastal waters – and are threatened by lack of legal protection. We examined 12 intermittent streams in the temperate, humid climate of the Northeast USA. Over three years of monitoring, continuous flow was observed a median of 277 d yr-1, with no-flow conditions from early summer into fall. Estimated median discharge was 2.9 L s-1 or 0.36 mm d-1. All intermittent streams originated from source wetlands (median area: 0.27 ha) and the median length of the intermittent stream from the source wetland to the downstream perennial stream was 344 m. Through regional geospatial analysis with high resolution orthophotography, we estimated that widely available, “high resolution” (1:24,000) hydrography databases (e.g., NHDPlus HR) only displayed 43% of the total number of intermittent streams. Whole-stream gross nitrate-N uptake rates were estimated at six intermittent streams during continuous flow conditions using pulse additions of nitrate and a conservative tracer. These rates displayed high temporal variability (range: no detect to over 6000 mg N m-1 d-1); hot moments were noted in nine of the 65 pulse additions. Whole-stream gross nitrate-N uptake rates were significantly inversely related to discharge, with no measurable rates above 7 L s-1. Temperature was significantly positively correlated with whole-stream gross nitrate-N uptake rates, with more hot moments in the spring. Microbial assays demonstrated that nitrate cycling in intermittent streams are consistent with results from low order, perennial forested streams and highlighted the importance of debris dams and pools – potential locations for transient storage. Our assessment suggests that intermittent streams in our region may annually contribute 24-47% of the flow to perennial streams and potentially remove 4.1 to 80.4 kg nitrate-N km-2 annually. If development in these areas continues, perennial streams are in danger of losing a portion of their headwaters and potential nitrate uptake areas may become nitrate sources to downstream areas. These results argue to manage fluvial systems with a holistic approach that couples intermittent and perennial components.

Ruminant urine patch nitrification and N2O flux: effects of urine aucubin rate in a laboratory trial

ABSTRACTLivestock urine deposition onto grazed New Zealand pastures drives soil nitrous oxide (N2O) emissions. Urine patch N2O emissions can be reduced by inhibiting nitrification, a key urine patch nitrogen (N) transformation pathway. Aucubin, a secondary metabolite found in the pasture herb species plantain (Plantago lanceolata), is a potential nitrification inhibitor and could be excreted in urine by animals grazing plantain. In this laboratory trial, three rates of aucubin application (10, 50, and 100% of the highest theoretical aucubin excretion rate from cows grazing 100% plantain pasture) were added to urine and assessed for their potential to inhibit nitrification and subsequent N2O emissions. Significantly reduced N2O flux and soil concentrations, aligned with significantly increased soil and soil surface pH, indicated that aucubin inhibited nitrification from 5 to 17 days after urine application. However, this period of inhibition was not sufficient to reduce overall N2O emissions during the 35 day experiment.

“Candidatus Accumulibacter delftensis”: A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate

Populations of “Candidatus Accumulibacter”, a known polyphosphate-accumulating organism, within clade IC have been proposed to perform anoxic P-uptake activity in enhanced biological phosphorus removal (EBPR) systems using nitrate as electron acceptor. However, no consensus has been reached on the ability of “Ca. Accumulibacter” members of clade IC to reduce nitrate to nitrite. Discrepancies might relate to the diverse operational conditions which could trigger the expression of the Nap and/or Nar enzyme and/or to the accuracy in clade classification. This study aimed to assess whether and how certain operational conditions could lead to the enrichment and enhance the denitrification capacity of “Ca. Accumulibacter” within clade IC. To study the potential induction of the denitrifying enzyme, an EBPR culture was enriched under anaerobic–anoxic–oxic (A2O) conditions that, based on fluorescence in situ hybridization and ppk gene sequencing, was composed of around 97% (on a biovolume basis) of affiliates of “Ca. Accumulibacter” clade IC. The influence of the medium composition, sludge retention time (SRT), polyphosphate content of the biomass (poly-P), nitrate dosing approach, and minimal aerobic SRT on potential nitrate reduction were studied. Despite the different studied conditions applied, only a negligible anoxic P-uptake rate was observed, equivalent to maximum 13% of the aerobic P-uptake rate. An increase in the anoxic SRT at the expenses of the aerobic SRT resulted in deterioration of P-removal with limited aerobic P-uptake and insufficient acetate uptake in the anaerobic phase. A near-complete genome (completeness = 100%, contamination = 0.187%) was extracted from the metagenome of the EBPR biomass for the here-proposed “Ca. Accumulibacter delftensis” clade IC. According to full-genome-based phylogenetic analysis, this lineage was distant from the canonical “Ca. Accumulibacter phosphatis”, with closest neighbor “Ca. Accumulibacter sp. UW-LDO-IC” within clade IC. This was cross-validated with taxonomic classification of the ppk1 gene sequences. The genome-centric metagenomic analysis highlighted the presence of genes for assimilatory nitrate reductase (nas) and periplasmic nitrate reductase (nap) but no gene for respiratory nitrate reductases (nar). This suggests that “Ca. Accumulibacter delftensis” clade IC was not capable to generate the required energy (ATP) from nitrate under strict anaerobic-anoxic conditions to support an anoxic EBPR metabolism. Definitely, this study stresses the incongruence in denitrification abilities of “Ca. Accumulibacter” clades and reflects the true intra-clade diversity, which requires a thorough investigation within this lineage.

Responses of ammonia-oxidizers and comammox to different long-term fertilization regimes in a subtropical paddy soil

Nitrogen, including ammonium, is an essential nutrient for plant growth and heavily applied in agricultural systems via fertilization. Nitrification is a two-step microbiologically-mediated process in which ammonium is first oxidized to nitrite and then subsequently to nitrate. The objective of this study was to determine the influence of variable long-term (28 years) fertilization on the potential nitrification rate (PNR) and three prokaryotic groups involved in this process: (1) ammonium-oxidizing bacteria (AOB), (2) ammonium-oxidizing archaea (AOA), and (3) recently discovered bacteria with the capacity to perform complete nitrification (comammox). Fertilization treatments included urea ((NH2)2CO) only (N), urea ((NH2)2CO) + potassium sulfate (K2SO4) (NK), urea ((NH2)2CO) +calcium superphosphate (CaP2H4O8) +potassium sulfate (K2SO4) (NPK), and a control with no N. The PNR increased with N fertilization, indicating that N application accelerated soil nitrification. The lower AOB abundance, the highest AOA/AOB ratios and lower PNR were observed in the NK treatment compared to N and NPK treatments, suggesting that AOB may be the key driver of nitrification in this soil. Comammox had higher amoA gene abundance (2.72 × 107gene copies g−1 to 2.35 × 108 gene copies g−1 dry soil) than AOB and AOA for all treatments. The abundance of comammox clade A (7.38 × 107 gene copies g−1 -2.35 × 108 gene copies g−1 dry soil) was significantly higher than for comammox clade B (5.66 × 106 gene copies g−1 -1.42 × 107gene copies g−1 dry soil), and based on high abundance values, we suppose that comammox are non-negligible contributors to soil nitrification resulting from responsiveness to N fertilization.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg−1 dry sediment day−1 during the period of 15–90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg−1 dry sediment day−1. The denitrification gene abundances of the N-cycling genes were 107-108 orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 105-106 orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

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

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

Roots Mediate the Effects of Snowpack Decline on Soil Bacteria, Fungi, and Nitrogen Cycling in a Northern Hardwood Forest.

Rising winter air temperature will reduce snow depth and duration over the next century in northern hardwood forests. Reductions in snow depth may affect soil bacteria and fungi directly, but also affect soil microbes indirectly through effects of snowpack loss on plant roots. We incubated root exclusion and root ingrowth cores across a winter climate-elevation gradient in a northern hardwood forest for 29 months to identify direct (i.e., winter snow-mediated) and indirect (i.e., root-mediated) effects of winter snowpack decline on soil bacterial and fungal communities, as well as on potential nitrification and net N mineralization rates. Both winter snowpack decline and root exclusion increased bacterial richness and phylogenetic diversity. Variation in bacterial community composition was best explained by differences in winter snow depth or soil frost across elevation. Root ingrowth had a positive effect on the relative abundance of several bacterial taxonomic orders (e.g., Acidobacterales and Actinomycetales). Nominally saprotrophic (e.g., Saccharomycetales and Mucorales) or mycorrhizal (e.g., Helotiales, Russalales, Thelephorales) fungal taxonomic orders were also affected by both root ingrowth and snow depth variation. However, when grouped together, the relative abundance of saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi were not affected by root ingrowth or snow depth, suggesting that traits in addition to trophic mode will mediate fungal community responses to snowpack decline in northern hardwood forests. Potential soil nitrification rates were positively related to ammonia-oxidizing bacteria and archaea abundance (e.g., Nitrospirales, Nitrosomondales, Nitrosphaerales). Rates of N mineralization were positively and negatively correlated with ectomycorrhizal and saprotrophic fungi, respectively, and these relationships were mediated by root exclusion. The results from this study suggest that a declining winter snowpack and its effect on plant roots each have direct effects on the diversity and abundance of soil bacteria and fungal communities that interact to determine rates of soil N cycling in northern hardwood forests.