Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil

Benefits and limits of biological nitrification inhibitors for plant nitrogen uptake and the environment

Plant growth and high yields are secured by intensive use of nitrogen (N) fertilizer, which, however, pollutes the environment, especially when N is in the form of nitrate. Ammonium is oxidized to nitrate by nitrifiers, but roots can release biological nitrification inhibitors (BNIs). Under what conditions does root-exudation of BNIs facilitate nitrogen N uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant's life cycle. We determined the sensitivity of N uptake and loss to variations in the parameter values, testing a broad range of soil-plant-microbial conditions, including concentrations, diffusion, sorption, nitrification, population growth, and uptake kinetics. An increase in BNI exudation reduces net N loss and, under most conditions, increases plant N uptake. BNIs decrease uptake in the case of (1) low ammonium concentrations, (2) high ammonium adsorption to the soil, (3) rapid nitrate- or slow ammonium uptake by the plant, and (4) a slowly growing or (5) fast-declining nitrifier population. Bactericidal inhibitors facilitate uptake more than bacteriostatic ones. Some nitrification, however, is necessary to maximize uptake by both ammonium and nitrate transporter systems. An increase in BNI exudation should be co-selected with improved ammonium uptake. BNIs can reduce N uptake, which may explain why not all species exude BNIs but have a generally positive effect on the environment by increasing rhizosphere N retention.

Geochemical factors impacting nitrifying communities in sandy sediments

Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.

Synthesis of artificial humic acid-urea complex improves nitrogen utilization

The inefficient use of conventional nitrogen (N) fertilizers leads to N enrichment in the soil, resulting in N loss via runoff, volatilization and leaching. While using artificial humic acid to prepare novel N fertilizer is a good choice to improve its efficiency, the high heterogeneity of artificial humic acid limits its structural analysis and utilization efficiency. To solve above problems, this work mainly carried out the fractionation experiments, melt penetration experiments and soil incubation experiments. The results revealed that four fractions with different aromatization degree and molecular weights were obtained by the newly proposed continuous dissolution method, particular in the extraction solution of pH = 3-4, which were extracted with the highest aromatization degree. Furthermore, artificial humic acid urea complex fertilizers prepared at pH = 3-4 significantly improved the release of NH4+-N by 38.32% on days 7 and NO3--N by 10.30% on days 14, compared to urea application. The highly aromatic complex fertilizer with loading of urea-N was able to supply more inorganic N to the soil on days 3-14 (low molecular weight N) and to maintain a higher N content on days 70 (highly aromatized N). This can partially offset the mineralization of readily available organic N, buffering the immobilization of inorganic N from the soil when unstable organic compounds (e.g. conventional urea) were incorporated. A-HAU3-4 addition on days 70, Proteobacteria and Actinobacteriota were found to be the dominant phylum in the soil and the relative abundance of Endophytic bacteria was increased, which was conducive to the improvement of soil N utilization efficiency and soil N sequestration. Therefore, the preparation of artificial humic urea fertilizer with high aromatization degree or low molecular weight were an effective way to improve N utilization efficiency in the initial stages of soil incubation and maintain N fixation in the later stages of soil incubation. The future application of the strategy presented by this study would have an important ecological significance for alleviating agricultural N pollution.

Spatial and temporal changes in the assembly mechanism and co-occurrence network of the chromophytic phytoplankton communities in coastal ecosystems under anthropogenic influences

As a typical semiclosed coastal sea area in China, the ecological environment of Bohai Bay has been significantly disturbed by human activities. As primary producers, the chromophytic phytoplankton are the basis of ecosystems, especially in coastal ecosystems, and changes in the chromophytic phytoplankton community can affect the stability of the entire ecosystem. In this study, we investigated the effects of the human activity-induced spatial and temporal environmental heterogeneity on the community composition, diversity, assembly mechanisms, and co-occurrence networks of chromophytic phytoplankton in Bohai Bay during the wet season and the dry season. The results showed that in both seasons, there was obvious environmental heterogeneity between the nearshore area and the offshore area, and the nearshore areas were more affected by human disturbance. Although higher diversity was supported by the abundance of nutrients in nearshore areas, co-occurrence network analysis revealed that the chromophytic phytoplankton were less closely connected to each other in nearshore areas than in offshore areas due to chemical oxygen demand (COD), eutrophication index (EI), and dissolved inorganic nitrogen (DIN). The nearshore network was less stable than the offshore co-occurrence network in both seasons, which was related to the concentration of dissolved oxygen and COD. Both stochastic and deterministic processes dominated the assembly of the chromophytic phytoplankton communities, with different importance rankings of stochastic and deterministic processes in the nearshore and offshore areas. Drift dominated the assembly of the communities in nearshore areas, while variable selection dominated the assembly of the communities in offshore areas. DIN, EI, and COD, rather than geographic distance, were the main environmental factors affecting the phylogenetic turnover of the chromophytic phytoplankton. Our study showed that environmental heterogeneity caused by human disturbance had a greater impact on the chromophytic phytoplankton communities in Bohai Bay than natural factors such as temperature and salinity.

Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants

The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.

Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective

Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in the habitat heterogeneity in the two Haloxylon species from a nutrient perspective. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0-20, 20-40, and 40-60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g., eukarya, bacteria, and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil available nitrogen, especially nitrate nitrogen, was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g., Firmicutes, Bacteroidetes, and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. Haloxylon persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea), and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.

Identification of mutations in SARS-CoV-2 PCR primer regions

Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.

Response of soil microbial communities to petroleum hydrocarbons at a multi-contaminated industrial site in Lanzhou, China

Total petroleum hydrocarbon (TPH) contamination poses threats to ecological systems and human health. Many studies have reported its negative impacts on soil microbes, but limited information is known about microbial change and response to multiple TPH contamination events. In this study, we investigated TPH contamination level, microbial community structure and functional genes at a multi-contaminated industrial site in Lanzhou, where a benzene spill accident caused the drinking water crisis in 2014. TPHs distribution in soils and groundwater indicated multiple TPH contamination events in history, and identified the spill location where high TPH level (6549 mg kg^-1) and high ratio of low-molecular-weight TPHs (>80%) were observed. In contrast, TPH level was moderate (349 mg kg^-1) and the proportion of low-molecular-weight TPHs was 44% in soils with a long TPH contamination history. After the spill accident, soil bacterial communities became significant diverse (p = 0.047), but the dominant microbes remained the same as Pseudomonadaceae and Comamonadaceae. The abundance of hydrocarbon-degradation related genes increased by 10-1000 folds at the site where the spill accident occurred in multi-contaminated areas and was significantly related to 2-ring PAHs. Such changes of microbial community and hydrocarbon-degradation related genes together indicated the resilience of soil indigenous microbes toward multiple contamination events. Our results proved the significant change of bacterial community and huge shift of hydrocarbon-degradation related genes after the spill accident (multiple contamination events), and provided a deep insight into microbial response at industrial sites with a long period of contamination history.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions

Background

Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification.

Materials and Methods

A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively.

Results and discussions

Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH₃ concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH₄ ⁺ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA.

Conclusions

PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH₄ ⁺, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.

A Technique for Rapid Bacterial-Density Enumeration through Membrane Filtration and Differential Pressure Measurements

In this article, we present a microfluidic technique for the rapid enumeration of bacterial density with a syringe filter to trap bacteria and the quantification of the bacterial density through pressure difference measurement across the membrane. First, we established the baseline differential pressure and hydraulic resistance for a filtration membrane by fully wetting the filter with DI water. Subsequently, when bacteria were infused and trapped at the pores of the membrane, the differential pressure and hydraulic resistance also increased. We characterized the infusion time required for the bacterial sample to achieve a normalized hydraulic resistance of 1.5. An equivalent electric-circuit model and calibration data sets from parametric studies were used to determine the general form of a calibration curve for the prediction of the bacterial density of a bacterial sample. As a proof of concept, we demonstrated through blind tests with Escherichia coli that the device is capable of determining the bacterial density of a sample ranging from 7.3 × 10⁶ to 2.2 × 10⁸ CFU/mL with mean and median accuracies of 87.21% and 91.33%, respectively. The sample-to-result time is 19 min for a sample with lower detection threshold, while for higher-bacterial-density samples the measurement time is further shortened to merely 8 min.

A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria

Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N₂O) and perform the first step of nitrification, but their contribution to N₂O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N₂O emissions and increased 71.4% of soil NH4+ concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N₂O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N₂O emissions with NI addition was significantly correlated with AOB changes (R² = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in NH4+ concentration and AOB amoA gene abundance after NI application (R² = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.

Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency

Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.

Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization

Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha^-1 yr^-1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha^-1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 10⁷ to 1.05 × 10⁷ copies g^-1 dry soil, while AOB abundance increased from 3.63 × 10⁷ up to a maximum of 8.24 × 10⁷ copies g^-1 dry soil with the N105 treatment (105 kg N ha^-1 yr^-1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH₄-N, and NO₃-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH₄-N for the AOB community. Overall, 105 kg N ha^-1 yr^-1 was optimum for the AOB community and wheat yield in the semi-arid area.

Combined impact of TiO2 nanoparticles and antibiotics on the activity and bacterial community of partial nitrification system

The effects of TiO2 nanoparticles (nano-TiO2) together with antibiotics leaking into wastewater treatment plants (WWTPs), especially the partial nitrification (PN) process remain unclear. To evaluate the combined impact and mechanisms of nano-TiO2 and antibiotics on PN systems, batch experiments were carried out with six bench-scale sequencing batch reactors. Nano-TiO2 at a low level had minimal effects on the PN system. In combination with tetracycline and erythromycin, the acute impact of antibiotics was enhanced. Both steps of nitrification were retarded due to the decrease of bacterial activity and abundance, while nitrite-oxidizing bacteria were more sensitive to the inhibition than ammonia-oxidizing bacteria. Proteobacteria at the phylum level and Nitrosospira at the genus level remained predominant under single and combined impacts. The flow cytometry analysis showed that nano-TiO2 enhanced the toxicity of antibiotics through increasing cell permeability. Our results can help clarify the risks of nano-TiO2 combined with antibiotics to PN systems and explaining the behavior of nanoparticles in WWTPs.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

Nitrous oxide production from soybean and maize under the influence of weedicides and zero tillage conservation agriculture

Current experiment envisages evaluating N2O production from nitrification and denitrification under the influence of weedicides, cropping systems and conservation agriculture (CA). The weed control treatments were conventional hand weeding (no weedicide), pre emergence weedicide pendimethalin and post emergence weedicide imazethapyr for soybean, atrazine for maize. Experiment was laid out in randomized block design with three replicates. Soils were collected from different depths and incubated at different moisture holding capacity (MHC). N2O production from nitrification varied from 2.77 to 6.04 ng N2O g-1 soil d-1 and from denitrification varied from 0.05 to 1.34 ng N2O g-1 soil d-1. Potential nitrification rate (0.16-0.39 mM NO3 produced g-1 soil d-1) was higher than potential denitrification rate (0.45-0.93 mM NO3 reduced g-1 soil d-1). N2O production, nitrification, denitrification, and microbial gene abundance were higher in maize than soybean. Both N2O production and nitrification decreased (p < 0.05) with soil depth, while denitrification increased (p < 0.05) with soil depth. Abundance of eubacteria and ammonia oxidizing bacteria (AOB) were high (p < 0.01) at upper soil layer and declined with depth. Abundance of ammonia oxidizing archaea (AOA) increased (p < 0.05) with soil depth. Study concludes that intensive use of weedicides in CA may stimulate N2O production.

Towards a mechanistic understanding of soil nitrogen availability responses to summer vs. winter drought in a semiarid grassland

More frequent and intense drought events resulting from climate change are anticipated to become important drivers of change for terrestrial ecosystem function by affecting water and nutrient cycles. In semiarid grasslands, the responses of soil nitrogen availability to severe drought and the underlying mechanisms are largely unknown. Moreover, the responses and mechanisms may vary between summer and winter drought. We examined soil nitrogen availability responses to extreme reductions in precipitation over summer and winter using a field experiment in a semiarid grassland located in northeast China, and we explored the mechanisms by examining associated changes in abiotic factors (soil property responses) and biotic factors (plant and soil microbial responses). The results demonstrated that both the summer and winter severe drought treatments significantly reduced plant and microbial biomass, whereas summer drought also changed soil microbial community structure. Summer drought, winter drought and combined summer and winter drought decreased the resistance of soil nitrogen availability by 38.7 ± 11.1%, 43.3 ± 11.4% and 43.8 ± 6.0%, respectively. While both changes in abiotic factors (reduced soil water content and total nitrogen content) and biotic factors (reduced plant and microbial biomass) explained the resistance of soil nitrogen availability to drought over summer, only changes in biotic factors (reduced plant and microbial biomass) explained the legacy effect of winter drought. Our results highlight that severe drought can have important consequences for nitrogen cycling in semiarid grasslands, and that both the effects of summer and winter drought must be accounted for in predicting these responses.

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

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

Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe

The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.

Response Characteristics of Nitrifying Bacteria and Archaea Community Involved in Nitrogen Removal and Bioelectricity Generation in Integrated Tidal Flow Constructed Wetland-Microbial Fuel Cell

This study explores nitrogen removal performance, bioelectricity generation, and the response of microbial community in two novel tidal flow constructed wetland-microbial fuel cells (TFCW-MFCs) when treating synthetic wastewater under two different chemical oxygen demand/total nitrogen (COD/TN, or simplified as C/N) ratios (10:1 and 5:1). The results showed that they achieved high and stable COD, NH₄ ⁺-N, and TN removal efficiencies. Besides, TN removal rate of TFCW-MFC was increased by 5-10% compared with that of traditional CW-MFC. Molecular biological analysis revealed that during the stabilization period, a low C/N ratio remarkably promoted diversities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the cathode layer, whereas a high one enhanced the richness of nitrite-oxidizing bacteria (NOB) in each medium; the dominant genera in AOA, AOB, and NOB were Candidatus Nitrosotenuis, Nitrosomonas, and Nitrobacter. Moreover, a high C/N ratio facilitated the growth of Nitrosomonas, while it inhibited the growth of Candidatus Nitrosotenuis. The distribution of microbial community structures in NOB was separated by space rather than time or C/N ratio, except for Nitrobacter. This is caused by the differences of pH, dissolved oxygen (DO), and nitrogen concentration. The response of microbial community characteristics to nitrogen transformations and bioelectricity generation demonstrated that TN concentration is significantly negatively correlated with AOA-shannon, AOA-chao, 16S rRNA V4-V5-shannon, and 16S rRNA V4-V5-chao, particularly due to the crucial functions of Nitrosopumilus, Planctomyces, and Aquicella. Additionally, voltage output was primarily influenced by microorganisms in the genera of Nitrosopumilus, Nitrosospira, Altererythrobacter, Gemmata, and Aquicella. This study not only presents an applicable tool to treat high nitrogen-containing wastewater, but also provides a theoretical basis for the use of TFCW-MFC and the regulation of microbial community in nitrogen removal and electricity production.

Linking nitrous oxide emissions from starch wastewater digestate amended soil to the abundance and structure of denitrifier communities

Anaerobic digestion is widely used in starch wastewater pre-treatment and can remove the COD effectively, however, the effluents are nutritious and often need supplemental aerobic treatments to remove nutrients prior to discharge. The objective of this study was to investigate the feasibility of using the liquid digestate of starch wastewater (LDSW) as a fertilizer. This pot experiment was conducted with Ipomoea aquatica Forsk in a greenhouse with six treatment groups. The crop growth was significantly promoted, while the accumulation of soil nitrate was not influenced after LDSW addition, compared to the control. In addition, at the same nitrogen input, the yield of high-LDSW treatment was 65.2%, 92.3% and 69.2% higher than those of chemical fertilizer treatment during the three growth periods. Furthermore, average N₂O emission with high-LDSW addition was 15.8 g N/(ha.d), accounting for 15.0% of which under high chemical fertilizer treatment, due to the significantly enhanced denitrification genes (nirK, nirS and nosZ) abundance. Besides, the changes of soil N₂O-reducing bacteria were performed by high-throughput sequencing of nosZ. Our findings suggested that LDSW had many opportunities for sustainable agriculture to guarantee high yields while reducing negative environmental impacts.

The distribution of functional N-cycle related genes and ammonia and nitrate nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Nitrogen transformation in soil is a complex process and the soil microbial population can regulate the potential for N mineralization, nitrification and denitrification. Here we show that agricultural soils under standard agricultural N-management are consistently characterized by a high presence of gene copies for some of the key biological activities related to the N-cycle. This led to a strong NO₃^- reduction (75%) passing from the soil surface (15.38 ± 11.36 g N-NO₃ kg^-1 on average) to the 1 m deep layer (3.92 ± 4.42 g N-NO₃ kg^-1 on average), and ensured low nitrate presence in the deepest layer. Under these circumstances the other soil properties play a minor role in reducing soil nitrate presence in soil. However, with excessive N fertilization, the abundance of bacterial gene copies is not sufficient to explain N leaching in soil and other factors, i.e. soil texture and rainfall, become more important in controlling these aspects.

Impact of Irrigation Strategies on Tomato Root Distribution and Rhizosphere Processes in an Organic System

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands

Aerobic ammonia oxidation, an important part of the global nitrogen cycle, is thought to be jointly driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in coastal wetlands. However, the activities and contributions of AOA and AOB in coastal wetlands have remained largely unknown. Here, we investigated the oxidation capability of AOA and AOB in four types of typical coastal wetlands (paddy, estuary, shallow and reed wetland) in the Bohai region in China using DNA-based stable-isotope probing (DNA-SIP), quantitative PCR and high-throughput sequencing techniques. We found that the community structure of AOB varied substantially, and the AOA structure was more stable across different coastal wetlands. The rate of AOA was 0.12, 0.84, 0.45 and 0.93 μg N g^-1 soil d^-1 in paddy, estuary, shallow and reed wetlands, and the rate of AOB was 5.61, 10.72, 0.74 and 1.16 μg N g^-1 soil d^-1, respectively. We found that the contribution of AOA gradually increased from paddy to estuary to shallow wetland and finally to reed wetland, with values of 2.03%, 7.25%, 37.53% and 44.51%, respectively. Our results provide new insight into the mechanisms of the differences in activities and the contributions of AOA and AOB in different coastal wetlands, and our findings may contribute to further understanding of the global nitrogen cycle.

Paenibacillus polymyxa biofertilizer application in a tea plantation reduces soil N2O by changing denitrifier communities

Increasing the use of nitrogen fertilizers in tea orchards has led to intense nitrous oxide (N₂O) emissions. Foliar application of Paenibacillus polymyxa biofertilizer has been proven to be beneficial for organic tea production. In this study, tea yield and quality were significantly improved after application of P. polymyxa biofertilizer compared with the control but were not significantly different from chemical fertilizer treatments. However, the average N₂O fluxes in tea fields treated with chemical fertilizers and biofertilizers (225 kg N·ha^-1·year^-1 for both) were 50.6-973.7 and 0.6-29.1 times higher than those in the control treatment, respectively. Pot experiments conducted to explore the mechanism of N₂O reduction induced by P. polymyxa biofertilizer showed that applying P. polymyxa in addition to urea could reduce N₂O fluxes by 36.5%-73.1%. Quantitative PCR analysis suggested that a significant increase in the quantity of nirK and nosZ genes was linked to the reduction of N₂O, and high-throughput sequencing of nosZ revealed active and potentially efficient denitrifiers in different treatments. Our findings suggest that P. polymyxa biofertilizer is in line with the requirements of modern agriculture, which aims to increase product yield and quality while reducing negative environmental impacts.

Detection and Quantification of Nitrifying Bacteria Using Real-Time PCR

Nitrification is the microbial-mediated transformation of ammonium (NH₄⁺) into nitrate (NO₃^-). Many plant species depend on the availability of NO₃^- as the main source of nitrogen (N). On the other hand, because NO₃^- is highly mobile in the soil profile, its excess concentration can cause environmental pollution. Nitrification can be estimated at the process level, but with the development of molecular techniques it is also possible to estimate the abundance of nitrifying bacteria in the soil. Hence, in this chapter we describe the procedure for detection and quantification of nitrifying bacteria in soil samples using real-time quantitative polymerase chain reaction (PCR).

Genetic associations as indices for assessing nitrogen transformation processes in co-composting of cattle manure and rice straw

In this study, mechanism of nitrogen transformation was investigated in terms of genetic associations (nitrogen-related gene groups) in co-composting of cattle manure and rice straw. Mutual validation among KEGG, Pearson correlation, stepwise regression, and Path analyses indicated that the functional genes synergistically affected on nitrogen transformation in composting process. NxrA/qnorB (0.9419 ± 0.0334) and (amoA + anammox)/Bacteria (0.7187 ± 0.0334) were the key functional gene groups mediating NH₄⁺-N transformation. AmoA/(narG + napA) (-0.8400 ± 0.0129), amoA/bacteria (0.8692 ± 0.0273), and (nirK + nirS)/nosZ (1.1652 ± 0.0089) determined NO₃^--N, NO₂^--N and N₂O transformation, respectively. AmoA/(napA + narG) mediated both NO₃^--N and NO₂^--N transformation. AmoA/anammox (-0.7172 ± 0.0591) and (nirK + nirS)/nosZ (-0.6626 ± 0.0825) served as predominant factors for total nitrogen removal. These results provided a molecular-level insight that nitrification, anaerobic ammonia oxidation and denitrification (SNAD) might simultaneously contribute to nitrogen transformation during composting, rather than sequentially.

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

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

Specific detection of Lysobacter antibioticus strains in agricultural soil using PCR and real-time PCR

Lysobacter antibioticus is an important biocontrol bacteria against phytopathogens in soil, and with the ability to produce nonvolatile antimicrobial metabolites has been extensively characterised. It is important to establish applicable techniques to detect and monitor L. antibioticus directly and accurately in soil samples. We developed and tested 13 primer sets according to phenazine gene (phzA, phzB, phzD, phzF, phzS) and the cyclohexanone monooxygenase gene (phzNO1); a pair of primer phzNO1 F1/phzNO1 R1 based on the cyclohexanone monooxygenase (phzNO1) gene of L. antibioticus strain OH13 was selected and optimized polymerase chain reaction (PCR) amplification conditions for rapid and accurate detection. After screening eight strains of L. antibioticus, two strains of Lysobacter enzymogenes, one strain of Lysobacter capsici, Arthrobacterium, Bacillus, Microbacterium, Burkholderia, Pseudomonas and other bacterial strains isolated from different agricultural soils, the phzNO1 F1/phzNO1 R1 primers amplified a single PCR band of about 229 bp from L. antibioticus. The detection sensitivity with primers phzNO1 F1/phzNO1 R1 was 5.14 × 104 fg/25μL of genomic DNA and 2.254 × 1010 to 2.254 × 1011 colony-forming units/mL for the soil samples. Quantitative PCR assays were to develope as a specific method to monitor the L. antibioticus population in soil as well as guide soil micro-ecological management.

Diversity and Spatial Distribution of Chromophytic Phytoplankton in the Bay of Bengal Revealed by RuBisCO Genes (rbcL)

Phytoplankton are the basis of primary production and play important roles in regulating energy export in marine ecosystems. Compared to other regions, chromophytic phytoplankton are considerably understudied in the Bay of Bengal (BOB). Here, we investigated community structure and spatial distribution of chromophytic phytoplankton in the BOB by using RuBisCO genes (Form ID rbcL). High throughput sequencing of rbcL genes revealed that diatoms, cyanobacteria (Cyanophyceae), Pelagophyceae, Haptophyceae, Chrysophyceae, Eustigamatophyceae, Xanthophyceae, Cryptophyceae, Dictyochophyceae, and Pinguiophyceae were the most abundant groups recovered in the BOB. Abundances and distribution of diatoms and Pelagophyceae were further verified using quantitative PCR analyses which showed the dominance of these groups near the Equator region (p < 0.01) where upwelling was likely the source of nutrients. Further, redundancy analysis demonstrated that temperature was an important environmental driver in structuring distributions of Cyanophyceae and dominant chromophytic phytoplankton. Morphological identification and quantification confirmed the dominance of diatoms, and also detected other cyanobacteria and dinoflagellates that were missing in our molecular characterizations. Pearson’s correlations of these morphologically identified phytoplankton with environmental gradients also indicated that nutrients and temperature were key variables shaping community structure. Combination of molecular characterization and morphological identification provided a comprehensive overview of chromophytic phytoplankton. This is the first molecular study of chromophytic phytoplankton accomplished in the BOB, and our results highlight a combination of molecular analysis targeting rbcL genes and microscopic detection in examining phytoplankton composition and diversity.

Nitrification Rates Are Affected by Biogenic Nitrate and Volatile Organic Compounds in Agricultural Soils

The processes regulating nitrification in soils are not entirely understood. Here we provide evidence that nitrification rates in soil may be affected by complexed nitrate molecules and microbial volatile organic compounds (mVOCs) produced during nitrification. Experiments were carried out to elucidate the overall nature of mVOCs and biogenic nitrates produced by nitrifiers, and their effects on nitrification and redox metabolism. Soils were incubated at three levels of biogenic nitrate. Soils containing biogenic nitrate were compared with soils containing inorganic fertilizer nitrate (KNO₃) in terms of redox metabolism potential. Repeated NH₄–N addition increased nitrification rates (mM NO₃^1- produced g^-1 soil d^-1) from 0.49 to 0.65. Soils with higher nitrification rates stimulated (p < 0.01) abundances of 16S rRNA genes by about eight times, amoA genes of nitrifying bacteria by about 25 times, and amoA genes of nitrifying archaea by about 15 times. Soils with biogenic nitrate and KNO₃ were incubated under anoxic conditions to undergo anaerobic respiration. The maximum rates of different redox metabolisms (mM electron acceptors reduced g^-1 soil d^-1) in soil containing biogenic nitrate followed as: NO₃^1- reduction 4.01 ± 0.22, Fe³⁺ reduction 5.37 ± 0.12, SO₄^2- reduction 9.56 ± 0.16, and CH₄ production (μg g^-1 soil) 0.46 ± 0.05. Biogenic nitrate inhibited denitrificaton 1.4 times more strongly compared to mineral KNO₃. Raman spectra indicated that aliphatic hydrocarbons increased in soil during nitrification, and these compounds probably bind to NO₃ to form biogenic nitrate. The mVOCs produced by nitrifiers enhanced (p < 0.05) nitrification rates and abundances of nitrifying bacteria. Experiments suggest that biogenic nitrate and mVOCs affect nitrification and redox metabolism in soil.

Effects of Oenanthe javanica on Nitrogen Removal in Free-Water Surface Constructed Wetlands under Low-Temperature Conditions

To investigate the role and microorganism-related mechanisms of macrophytes and assess the feasibility of Oenanthe javanica (Blume) DC. in promoting nitrogen removal in free-water surface constructed wetlands (FWS-CWS) under low temperatures (<10 °C), pilot-scale FWS-CWS, planted with O. javanica, were set up and run for batch wastewater treatment in eastern China during winter. The presence of macrophytes observably improved the removal rates of ammonia nitrogen (65%-71%) and total nitrogen (41%-48%) (p < 0.05), with a sharp increase in chemical oxygen demand concentrations (about 3-4 times). Compared to the unplanted systems, the planted systems not only exhibited higher richness and diversity of microorganisms, but also significantly higher abundances of bacteria, ammonia monooxygenase gene (amoA), nitrous oxide reductase gene (nosZ), dissimilatory cd1-containing nitrite reductase gene (nirS), and dissimilatory copper-containing nitrite reductase gene (nirK) in the substrate. Meanwhile, the analysis of the microbial community composition further revealed significant differences. The results indicate that enhanced abundances of microorganisms, and the key functional genes involved with nitrogen metabolism in the planted systems played critical roles in nitrogen removal from wastewater in FWS-CWS. Furthermore, abundant carbon release from the wetland macrophytes could potentially aid nitrogen removal in FWS-CWS during winter.

Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability

Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N₂ fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N₂ fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses

Advances in high-throughput sequencing have increased the availability of microbiome sequencing data that can be exploited to characterize microbiome community structure in situ. We explore using word and sentence embedding approaches for nucleotide sequences since they may be a suitable numerical representation for downstream machine learning applications (especially deep learning). This work involves first encoding ("embedding") each sequence into a dense, low-dimensional, numeric vector space. Here, we use Skip-Gram word2vec to embed k-mers, obtained from 16S rRNA amplicon surveys, and then leverage an existing sentence embedding technique to embed all sequences belonging to specific body sites or samples. We demonstrate that these representations are meaningful, and hence the embedding space can be exploited as a form of feature extraction for exploratory analysis. We show that sequence embeddings preserve relevant information about the sequencing data such as k-mer context, sequence taxonomy, and sample class. Specifically, the sequence embedding space resolved differences among phyla, as well as differences among genera within the same family. Distances between sequence embeddings had similar qualities to distances between alignment identities, and embedding multiple sequences can be thought of as generating a consensus sequence. In addition, embeddings are versatile features that can be used for many downstream tasks, such as taxonomic and sample classification. Using sample embeddings for body site classification resulted in negligible performance loss compared to using OTU abundance data, and clustering embeddings yielded high fidelity species clusters. Lastly, the k-mer embedding space captured distinct k-mer profiles that mapped to specific regions of the 16S rRNA gene and corresponded with particular body sites. Together, our results show that embedding sequences results in meaningful representations that can be used for exploratory analyses or for downstream machine learning applications that require numeric data. Moreover, because the embeddings are trained in an unsupervised manner, unlabeled data can be embedded and used to bolster supervised machine learning tasks.

Monochloramine dissipation in storm sewer systems: field testing and model development

Monochloramine (NH₂Cl), as the dominant disinfectant in drinking water chloramination, can provide long-term disinfection in distribution systems. However, NH₂Cl can also be discharged into storm sewer systems and cause stormwater contamination through outdoor tap water uses. In storm sewer systems, NH₂Cl dissipation can occur by three pathways: (i) auto-decomposition, (ii) chemical reaction with stormwater components, and (iii) biological dissipation. In this research, a field NH₂Cl dissipation test was conducted with continuous tap water discharge into a storm sewer. The results showed a fast decrease of NH₂Cl concentration from the discharge point to the sampling point at the beginning of the discharge period, while the rate of decrease decreased as time passed. Based on the various pathways involved in NH₂Cl decay and the field testing results, a kinetic model was developed. To describe the variation of the NH₂Cl dissipation rates during the field testing, a time coefficient f_T was introduced, and the relationship between f_T and time was determined. After calibration through the f_T coefficient, the kinetic model described the field NH₂Cl dissipation process well. The model developed in this research can assist in the regulation of tap water outdoor discharge and contribute to the protection of the aquatic environment.

Linking N2O Emissions from Biofertilizer-Amended Soil of Tea Plantations to the Abundance and Structure of N2O-Reducing Microbial Communities

Nitrous oxide (N₂O) contributes up to 8% of global greenhouse gas emissions, with approximately 70% from terrestrial sources; over one-third of this terrestrial emission has been linked to increased agricultural fertilizer use. Much of the nitrogen in fertilizers is converted to N₂O by microbial processes in soil. However, the potential mechanism of biofertilizers and the role of microbial communities in mitigating soil N₂O emissions are not fully understood. Here, we used a greenhouse-based pot experiment with tea plantation soil to investigate the effect of Trichoderma viride biofertilizer on N₂O emission. The addition of biofertilizer reduced N₂O emissions from fertilized soil by 67.6%. Quantitative PCR (qPCR) analysis of key functional genes involved in N₂O generation and reduction ( amoA, nirK, nirS, and nosZ) showed an increased abundance of nirS and nosZ genes linked to the pronounced reduction in N₂O emissions. High-throughput sequencing of nosZ showed enhanced relative abundance of nosZ-harboring denitrifiers in the T. viride biofertilizer treatments, thus linking greater N₂O reduction capacity to the reduced emissions. Our findings showed that biofertilizers can affect the microbial nitrogen transformation process and reduce N₂O emissions from agroecosystems.

Abundance and Diversity of Aerobic/Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms in an Ammonium-Rich Aquitard in the Pearl River Delta of South China

Natural occurring groundwater with abnormally high ammonium concentrations was discovered in the aquifer-aquitard system in the Pearl River Delta, South China. The community composition and abundance of aerobic/anaerobic ammonia/ammonium-oxidizing microorganisms (AOM) in the aquitard were investigated in this study. The alpha subunit of ammonia monooxygenase gene (amoA) was used as the biomarker for the detection of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), and also partial 16S rRNA gene for Plantomycetes and anaerobic ammonium-oxidizing (anammox) bacteria. Phylogenetic analysis showed that AOA in this aquitard were affiliated with those from water columns and wastewater treatment plants; and AOB were dominated by sequences among the Nitrosomonas marina/Nitrosomonas oligotropha lineage, which were affiliated with environmental sequences from coastal eutrophic bay and subtropical estuary. The richness and diversity of both AOA and AOB communities had very little variations with the depth. Candidatus Scalindua-related sequences dominated the anammox bacterial community. AOB amoA gene abundances were always higher than those of AOA at different depths in this aquitard. The Pearson moment correlation analysis showed that AOA amoA gene abundance positively correlated with pH and ammonium concentration, whereas AOB amoA gene abundance negatively correlated with C/N ratio. This is the first report that highlights the presence with low diversity of AOM communities in natural aquitard of rich ammonium.

Effect of clonal integration on nitrogen cycling in rhizosphere of rhizomatous clonal plant, Phyllostachys bissetii, under heterogeneous light

Clonal integration plays an important role in clonal plant adapting to heterogeneous habitats. It was postulated that clonal integration could exhibit positive effects on nitrogen cycling in the rhizosphere of clonal plant subjected to heterogeneous light conditions. An in-situ experiment was conducted using clonal fragments of Phyllostachys bissetii with two successive ramets. Shading treatments were applied to offspring or mother ramets, respectively, whereas counterparts were treated to full sunlight. Rhizomes between two successive ramets were either severed or connected. Extracellular enzyme activities and nitrogen turnover were measured, as well as soil properties. Abundance of functional genes (archaeal or bacterial amoA, nifH) in the rhizosphere of shaded, offspring or mother ramets were determined using quantitative polymerase chain reaction. Carbon or nitrogen availabilities were significantly influenced by clonal integration in the rhizosphere of shaded ramets. Clonal integration significantly increased extracellular enzyme activities and abundance of functional genes in the rhizosphere of shaded ramets. When rhizomes were connected, higher nitrogen turnover (nitrogen mineralization or nitrification rates) was exhibited in the rhizosphere of shaded offspring ramets. However, nitrogen turnover was significantly decreased by clonal integration in the rhizosphere of shaded mother ramets. Path analysis indicated that nitrogen turnover in the rhizosphere of shaded, offspring or mother ramets were primarily driven by the response of soil microorganisms to dissolved organic carbon or nitrogen. This unique in-situ experiment provided insights into the mechanism of nutrient recycling mediated by clonal integration. It was suggested that effects of clonal integration on the rhizosphere microbial processes were dependent on direction of photosynthates transport in clonal plant subjected to heterogeneous light conditions.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.

AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

Estimation of the influence of sequencing errors and distribution of random-sequence tags on quantitative sequencing

To simultaneously sequence and quantify target DNA, quantitative sequencing (qSeq) employs stochastic labeling of target DNA molecules with random-sequence tags (RSTs). This recently developed approach allows parallel quantification of hundreds of microorganisms in natural habitats in a single sequencing run. Yet, no study has addressed to what extent sequencing errors affect quantification and how many sequence reads are needed for quantification. Here, we addressed those issues by using numerical simulations and experimental data from second-generation sequencing of various RSTs. We found that heterogeneous distribution of observed RSTs affected the number of sequence reads required to quantitate target genes, whereas the effect of sequencing errors is smaller than of the RSTs distribution. Because of the heterogeneous RSTs distribution, 15-fold more sequence reads than the number of observed RSTs should be obtained to retrieve almost all RSTs needed for quantification; in that case, quantification error is estimated to be within 5%.

N2O emission characteristics and its affecting factors in rain-fed potato fields in Wuchuan County, China

Representing an important greenhouse gas, nitrous oxide (N₂O) emission from cultivated land is a hot topic in current climate change research. This study examined the influences of nitrogen fertilisation, temperature and soil moisture on the ammonia monooxygenase subunit A (amoA) gene copy numbers and N₂O emission characteristics. The experimental observation of N₂O fluxes was based on the static chamber-gas chromatographic method. The ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) gene copy numbers in different periods were measured by real-time polymerase chain reaction (PCR). The results indicated that rain-fed potato field was a N₂O source, and the average annual N₂O emission was approximately 0.46 ± 0.06 kgN₂O-N/ha/year. N₂O emissions increased significantly with increase in fertilisation, temperatures below 19.6 °C and soil volumetric water content under 15%. Crop rotation appreciably decreases N₂O emissions by 34.4 to 52.4% compared to continuous cropping in rain-fed potato fields. The significant correlation between N₂O fluxes and AOB copy numbers implied that N₂O emissions were primarily controlled by AOB in rain-fed potato fields. The research has important theoretical and practical value for understanding N₂O emissions from rain-fed dry farmland fields.

Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal

Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.

AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

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.

The effect of dissolved oxygen concentration (DO) on oxygen diffusion and bacterial community structure in moving bed sequencing batch reactor (MBSBR)

The effect of dissolved oxygen concentration (DO) on simultaneous nitrification and denitrification was studied in a moving bed sequencing batch reactor (MBSBR) by microelectrode measurements and by real-time PCR. In this system, the biofilm grew on polyurethane foam carriers used to treat municipal sewage at five DO concentrations (1.5, 2.5, 3.5, 4.5 and 5.5 mg/L). The results indicated that the MBSBR exhibited good removal of chemical oxygen demand (92.43%) and nitrogen (83.73%) when DO concentration was 2.5 mg/L. Increasing the oxygen concentration in the reactor was inhibitory to denitrification. Microelectrode measurements showed that the thickness of oxygen penetration increased from 1.2 to 2.6 mm when the DO concentration (from 1.5 mg/L to 5.5 mg/L) in the system increased. Oxygen diffusion was not significantly limited by the boundary layer surrounding the carrier and had the largest slope when DO concentration was 2.5 mg/L. The real-time PCR analysis indicated that the amount of the ammonia-oxidizing bacteria and nitrite-oxidizing bacteria increased slowly as DO concentration increased. The proportions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria, as a percentage of the total bacteria, were low with average values of 0.063% and 0.67%, respectively. When the DO concentration was 2.5 mg/L, oxygen diffusion was optimal and ensured the optimal bacterial community structure and activity; under these conditions, the MBSBR was efficient for total inorganic nitrogen removal. Changing the DO concentration could alter the aerobic zone and the bacterial community structure in the biofilm, directly influencing the simultaneous nitrification and denitrification activity in MBSBRs.

An improved protocol with a highly degenerate primer targeting copper-containing membrane-bound monooxygenase genes for community analysis of methane- and ammonia-oxidizing bacteria

The copper-containing membrane-bound monooxygenase (CuMMO) family comprises key enzymes for methane or ammonia oxidation: particulate methane monooxygenase (PMMO) and ammonia monooxygenase (AMO). To comprehensively amplify CuMMO genes, a two-step PCR strategy was developed using a newly designed tagged highly degenerate primer (THDP; degeneracy = 4608). Designated THDP-PCR, the technique consists of primary CuMMO gene-specific PCR followed by secondary PCR with a tag as a single primer. No significant bias in THDP-PCR amplification was found using various combinations of template mixtures of pmoA and amoA genes, which encode key subunits of the pMMO and AMO enzymes, respectively, from different microbes. THDP-PCR was successfully applied to nine different environmental samples and revealed relatively high contents of complete ammonia oxidation (Comammox)-related bacteria and a novel group of the CuMMO family. The levels of freshwater cluster methanotrophs obtained by THDP-PCR were much higher than those obtained by conventional methanotroph-specific PCR. The THDP-PCR strategy developed in this study can be extended to other functional gene-based community analyses, particularly when the target gene sequences lack regions of high consensus for primer design.