Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs

This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.

Effects of temperature on nitrifying membrane-aerated biofilms: An experimental and modeling study

Temperature is known to have an important effect on the morphology and removal fluxes of conventional, co-diffusional biofilms. However, much less is known about the effects of temperature on membrane-aerated biofilm reactors (MABRs). Experiments and modeling were used to determine the effects of temperature on the removal fluxes, biofilm thickness and morphology, and biofilm microbial community structure of nitrifying MABRs. Steady state tests were carried out at 10 °C and 30 °C. MABRs grown at 30 °C had higher ammonium removal fluxes (5.5 ± 0.9 g-N/m2/day at 20 mgN/L) than those grown at 10 °C (3.4 ± 0.2 g-N/m2/day at 20 mgN/L). The 30 °C biofilms were thinner and rougher, with a lower protein to polysaccharides ratio (PN/PS) in their extracellular polymeric substance (EPS) matrix and greater amounts of biofilm detachment. Based on fluorescent in-situ hybridization (FISH), there was a higher relative abundance of nitrifying bacteria at 30 °C than at 10 °C, and the ratio of AOB to total nitrifiers (AOB + NOB) was higher at 30 °C (95.1 ± 2.3%) than at 10 °C (77.2 ± 8.6 %). Anammox bacteria were more abundant at 30 °C (16.6 ± 3.7 %) than at 10 °C (6.5 ± 2.4 %). Modeling suggested that higher temperatures increase ammonium oxidation fluxes when the biofilm is limited by ammonium. However, fluxes decrease when oxygen becomes limited, i.e., when the bulk ammonium concentrations are high, due to decreased oxygen solubility. Consistent with the experimental results, the model predicted that the percentage of AOB to total nitrifiers at 30 °C was higher than at 10 °C. To investigate the effects of temperature on biofilm diffusivity and O2 solubility, without longer-term changes in the microbial community, MABR biofilms were grown to steady state at 20 °C, then the temperature changed to 10 °C or 30 °C overnight. Higher ammonium oxidation fluxes were obtained at higher temperatures: 1.91 ± 0.24 g-N/m2/day at 10 °C and 3.19 ± 0.40 g-N/m2/day at 30 °C. Overall, this work provides detailed insights into the effect of temperature on nitrifying MABRs, which can be used to better understand MABR behavior and manage MABR reactors.

Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge

In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process

Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.

Effects of nitrification and urease inhibitors on ammonia-oxidizing microorganisms, denitrifying bacteria, and greenhouse gas emissions in greenhouse vegetable fields

Soil microorganisms and N cycling are important components of biogeochemical cycling processes. In addition, the study of the effects of nitrification and urease inhibitors on N and microorganisms in greenhouse vegetable fields is essential to reducing N loss and greenhouse gas emissions. The effects of nitrification inhibitors [2-chloro-6-(trichloromethyl) pyridine (CP), dicyandiamide (DCD)], and urease inhibitor [N-(n-butyl) thiophosphoric triamide (NBPT)] on soil inorganic N (NH4+-N, NO2--N and NO3--N) concentrations and the production rates of greenhouse gases (N2O, CH4, and CO2) in greenhouse vegetable fields were investigated via indoor incubation experiments. Polymerase chain reaction amplification and high-throughput sequencing technology (Illumina Miseq) were used to explore the community structure and abundance changes of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifying bacteria (nirK and nirS). The results showed that CP and DCD obviously inhibited NH4+-N conversion, and NO2--N, and NO3--N accumulation, NBPT slowed down urea hydrolysis and NH4+-N production, and the apparent nitrification rates of soil were in the following order: NBPT > DCD > DCD + NBPT > CP + NBPT > CP. Compared with urea treatment, the peak N2O production rate of inhibitor treatment decreased by 73.30-99.30%, and the production rate of CH4 and CO2 decreased by more than 66.16%. DCD and CP reduced the abundance of AOA and AOB, respectively. Furthermore, NBPT hindered the growth of ammonia-oxidizing microorganisms and nirS-type denitrifying bacteria, and urea and nitrification inhibitors were detrimental to the growth of Ensifer and Sinorhizobium in the nirK community. Nitrification and urease inhibitors can effectively slow down nitrification and greenhouse gas emissions, reduce N loss and improve soil quality by inhibiting the growth of ammonia-oxidizing microorganisms and denitrifying bacteria.

Immediate response of paddy soil microbial community and structure to moisture changes and nitrogen fertilizer application

Water and fertilizer managements are the most common practices to maximize crop yields, and their long-term impact on soil microbial communities has been extensively studied. However, the initial response of microbes to fertilization and soil moisture changes remains unclear. In this study, the immediate effects of nitrogen (N)-fertilizer application and moisture levels on microbial community of paddy soils were investigated through controlled incubation experiments. Amplicon sequencing results revealed that moisture had a stronger influence on the abundance and community composition of total soil bacteria, as well as ammonia oxidizing-archaea (AOA) and -bacteria (AOB). Conversely, fertilizer application noticeably reduced the connectivity and complexity of the total bacteria network, and increasing moisture slightly exacerbated these effects. NH4+-N content emerged as a significant driving force for changes in the structure of the total bacteria and AOB communities, while NO3--N content played more important role in driving shifts in AOA composition. These findings indicate that the initial responses of microbial communities, including abundance and composition, and network differ under water and fertilizer managements. By providing a snapshot of microbial community structure following short-term N-fertilizer and water treatments, this study contributes to a better understanding of how soil microbes respond to long-term agriculture managements.

Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils

Introduction

Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils.

Methods

In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences.

Results

The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type.

Discussion

Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.

Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA-Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant

In this study, we explore the relationship between community structure and transcriptional activity of ammonia-oxidizing bacteria during cold temperature nitrification failure in three parallel full-scale sequencing batch reactors (SBRs) treating municipal wastewater. In the three reactors, ammonia concentrations increased with declines in wastewater temperature below 15°C. We quantified and sequenced 16S rRNA and ammonia monooxygenase (amoA) gene fragments in DNA and RNA extracts from activated sludge samples collected from the SBRs during the warmer seasons (summer and fall) and when water temperatures were below 15°C (winter and spring). Taxonomic community composition of amoA genes and transcripts did not vary much between the warmer and colder seasons. However, we observed significant differences in amoA transcript copy numbers between fall (highest) and spring (lowest). Ammonia-oxidizing bacteria of the genus Nitrosomonas sp. could maintain their population abundance despite lowering their amoA gene expression during winter and spring. In spite of relatively low population abundance, an amoA amplicon sequence variant (ASV) cluster identified as most similar to the amoA gene of Nitrosospira briensis showed the highest amoA transcript-to-gene ratio throughout all four seasons, indicating that some nitrifiers remain active at wastewater temperatures below 15°C. Our results show that 16S rRNA and amoA gene copy numbers are limited predictors of cell activity. To optimize function and performance of mixed community bioprocesses, we need to collect high-resolution quantitative transcriptomic and potentially proteomic data to resolve the response of individual species to changes in environmental parameters in engineered systems. IMPORTANCE The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. "Seasonal nitrification failure" is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C). This study aims at expanding our understanding of how ammonia-oxidizing bacteria in activated sludge change in activity and growth across seasons. We quantified the ammonia monooxygenase (amoA) gene and transcript copy numbers using real-time PCR and sequenced the amoA amplicons to reveal community structure and activity changes of nitrifying microbial populations during seasonal nitrification failure in three full-scale sequencing batch reactors (SRBs) treating municipal wastewater. Relevant findings presented in this study contribute to explain seasonal nitrification performance variability in SRBs.

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

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

Characteristics of soil N2O emission and N2O-producing microbial communities in paddy fields under elevated CO2 concentrations

The effects of elevated carbon dioxide (CO₂) concentration (e[CO₂]) on nitrous oxide (N₂O) emissions from paddy fields and the microbial processes involved in N₂O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N₂O in paddy soils. To better understand the dynamics of N₂O production under e[CO₂], a field experiment was conducted after five years of CO₂ fumigation based on three treatments: CK (ambient atmospheric CO₂), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N₂O fluxes, soil physicochemical properties, and N₂O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N₂O emissions decreased by 173% and 41% under the two e[CO₂] treatments during grain filling and milk ripening, respectively (P < 0.05). N₂O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N₂O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N₂O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N₂O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO₂], the abundance of nirK-type denitrifying bacteria significantly affected the N₂O flux (P < 0.05). Linear regression analysis showed that the N₂O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N₂O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO₂] suppressed N₂O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).

A new pattern of the partial nitrification and Anammox immobilized gel beads: core-shell embedded carrier

Single-stage partial nitrification and Anammox (PN/A) is an efficient and energy-saving denitrification process for wastewater. However, its application is limited by the growth conditions of microorganisms. Therefore, we improved the PN/A by developing a novel core-shell embedded carrier. With Anammox gel as the core and Ammonia-oxidizing bacteria gel as the shell, these beads can achieve dissolved oxygen partitioning and provide a suitable environment for the growth of different bacteria. On this basis, the influence of the shape of core-shell embedded gel on nitrogen removal performance was systematically studied, and the internal morphology and pore size of gel beads were characterized. The results showed that the nitrogen removal efficiency of spherical and square gels was increased by 33.70% and 13.47%, respectively, in the batch test. Fluorescence in situ hybridization confirmed the stratified growth of ammonia-oxidizing bacteria and Anammox in carriers, and the relative abundance value of the two bacteria were 1.25:1 and 1.43:1, respectively. Although the mechanical strength of square gel beads is slightly higher than that of spherical, spherical gel is considered the most suitable gel shape due to its small pore size and poor pore connectivity, which ensures the matching of internal Anammox and external PN reaction. In the long-term experiment, the core-shell embedded beads still had the design characteristics, and the TN removal efficiency was increased by 36.25% despite occasional oxygen excess.

Nitrosomonas supralitoralis sp. nov., an ammonia-oxidizing bacterium from beach sand in a supralittoral zone

A betaproteobacterial chemolithotrophic ammonia-oxidizing bacterium designated APG5^T was isolated from supralittoral sand of the Edmonds City Beach, WA, USA. Growth was observed at 10-35 °C (optimum, 30 °C), pH 5-9 (optimum, pH 8) and ammonia concentrations as high as 100 mM (optimum, 1-30 mM NH₄Cl). The strain grows optimally in a freshwater medium but tolerates up to 400 mM NaCl. It is most closely related to 'Nitrosomonas ureae' (96.7% 16S rRNA and 92.4% amoA sequence identity). The 3.75-Mbp of AGP5^T draft genome contained a single rRNA operon and all necessary tRNA genes and has the lowest G+C content (43.5%) when compared to the previously reported genomes of reference strains in cluster 6 Nitrosomonas. Based on an average nucleotide identity of 82% with its closest relative ('N. ureae' Nm10^T) and the suggested species boundary of 95-96%, a new species Nitrosomonas supralitoralis sp. nov. is proposed. The type strain of Nitrosomonas supralitoralis is APG5^T (= NCIMB 14870^T = ATCC TSD-116^T).

Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO₂^-, and NO₃^-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO₂^-, and NO₃^- are important shapers of nitrifier communities in mangroves.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Lab-scale data and microbial community structure suggest shortcut nitrogen removal as the predominant nitrogen removal mechanism in post-aerobic digestion (PAD)

Implementing an aerobic digestion step after anaerobic digestion, referred to as "post aerobic digestion" (PAD), can remove ammonia without the need for an external carbon source and destroy volatile solids. While this process has been documented at the lab-scale and full-scale, the mechanism for N removal and the corresponding microbial community that carries out this process have not been established. This research gap is important to fill because the nitrogen removal pathway has implications on aeration requirements and carbon demand, that is, short-cut N-removal requires less oxygen and carbon than simultaneous nitrification-denitrification. The aims of this research were to (i) determine if nitrite (NO₂ ^- ) or nitrate (NO₃ ^- ) dominates following ammonia removal and (ii) characterize the microbial community from PAD reactors. Here, lab-scale PAD reactors were seeded with biomass from two different full-scale PAD reactors. The lab-scale reactors were fed with biomass from full-scale reactors and operated in batch mode to quantify nitrogen species concentrations (ammonia, NH₄ ⁺ , NO₂ ^- , and NO₃ ^- ) over time. Experimental results revealed that NO₂ ^- production rates were several orders of magnitude greater than NO₃ ^- production rates. Indeed, nitrite accumulation rate (NAR) was greater than 90% at most temperatures, confirming that shortcut nitrogen removal was the dominant NH₄ ⁺ removal mechanism in PAD. Microbial community analysis via 16S rRNA sequencing indicated that ammonia oxidizing bacteria (AOB) were much more abundant than nitrite oxidizing bacteria (NOB). Overall, this study suggests that aeration requirements for post-aerobic digestion should be based on NO₂ ^- shunt and not complete simultaneous nitrification denitrification. PRACTITIONER POINTS: AOB are a key feature of PAD microbial communities NOB are present, but in much lower abundance than AOB High nitrite accumulation ratio suggests shortcut nitrite as the main mechanism for nitrogen removal Nitritation in PAD reactors is sustained at temperatures as high as 40°C No ammonia oxidation occurred at 50°C implying different mechanisms of nitrogen removal including ammonia stripping.

Symbiotic treatment of ammonia-nitrogen wastewater by algae and activated sludge: effects of algae and sludge inoculation rates

A symbiotic microalgal-bacterial system may be an optional technology for wastewater treatment. It was composed of microalgae and activated sludge and established in the SBR to explore the effect of different dosing ratios of algae and sludge on the removal of nitrogen and phosphorus from simulated wastewater containing ammonium. It can be seen from the result that varied algae-sludge dosing ratios had a higher removal effect on COD removal, but the difference was not significant. The algal-bacterial symbiosis system had a 100% removal rate for ammonium removal on the 8th day. Relatively speaking, the removal of nutrients and related mechanisms vary with environmental conditions (inoculation rate). In general, when the additive ratio was 5:1 (algae: AS), the removal rate of TN and TP was the highest, reaching 53.85% and 85.13% in the shortest time (14 days), among them, the removal rate of ammonium and COD was 100%, and the reduction rates of Nitrite nitrogen and Nitrate nitrogen were 362.99% and 73.42%, respectively. In addition, 16S rDNA gene analysis results demonstrated that the microbial community in the reactor with algal sludge inoculation ratio of 5:1 had differences in three stages of the initial reaction, the middle reaction and the end of the reaction. Comamonadaceae, Flavobacterium, Paenarthrobacter, Mesorhizobium, Nitrobacter were enriched during the reaction operation.

Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils

Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.

Assessing the influence of environmental niche segregation in ammonia oxidizers on N2O fluxes from soil and sediments

Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N₂O) production is essential for predicting N₂O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N₂O fluxes over pH (4.0-9.0) and temperature (10-45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N₂O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N₂O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N₂O fluxes decreased with increasing pH. Consequently, net N₂O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R² = 0.45, p < 0.01) between PAO and N₂O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N₂O fluxes, highlighting the potential for mitigating N₂O emissions via pH manipulation.

Effects of Methyl, Ester, and Amine Surface Groups on Microbial Activity and Communities in Nitrifying Biofilms

The objective of this study was to determine how different attachment surface chemistries affected the initial and long-term performance and microbial populations of nitrifying biofilms under well-controlled hydrodynamic mixing conditions. While much previous research has focused on the effects of surface properties such as hydrophobicity on bacterial attachment in pure cultures, this study evaluated the effects of specific functional groups on mixed culture composition and functional behavior. Three surfaces with varying hydrophobicity and charge were evaluated for biofilm community development and performance: unmodified poly(dimethylsiloxane) (PDMS), which included terminal methyl groups and was relatively hydrophobic (P-Methyl), PDMS silanized with ester groups (P-Ester), which was uncharged and relatively hydrophilic, and PDMS modified with amine groups (P-Amine), which possessed a positive charge and was the most hydrophilic. The surface chemistries of the three attachment surfaces were characterized by contact angle goniometry, Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). These surfaces were inoculated with dilute activated sludge, and biofilms were grown in rotating annular bioreactors for 80 days, with experimental triplicates. Nitrification rates increased most rapidly in P-Amine biofilm reactors, and their biofilm communities contained significantly more Nitrosomonas (p < 0.05) than those on the other surfaces in early growth stages (days 40-50). From days 50-60, the P-Amine surface biofilm had significantly higher nitrate production rates than the P-Methyl and P-Ester biofilms. The biofilms grown on the P-Amine and P-Methyl surfaces were significantly (p < 0.05) more diverse than the P-Ester biofilms, containing higher relative abundances of the order Rhizobiales, including a significantly higher abundance of the nitrifying genus Nitrobacter (p < 0.05), which coincided with higher rates of nitrate generation. Conversely, biofilms grown on the uncharged hydrophilic P-Ester surface were consistently less productive and had lower diversity than biofilms on the other surfaces. These results indicate that surface chemistry may be a useful design parameter to improve the performance of nitrifying biofilm systems for wastewater treatment and that surface chemistry affects mixed biofilm community composition.

Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental design criteria are rarely reported or overlooked. Here, we found that slight deviations in culture preparations and conditions impacted bacterial community performance and could skew assay results. From pre-experimental trials and experience, we determined how mishandling and treatment of cultures could affect nitrification activity. While media and biomass preparations are needed to establish baseline conditions (e.g., biomass washing), we found extensive centrifugation selectively destabilised nitrification activities. Further, it is paramount that the air supply is adjusted to minimise nitrite build-up in the culture and maintain suitable aeration levels without sparging ammonia. DMSO and acetone up to 0.03% (v/v) were suitable organic solvents with minimal impact on nitrification activity. In the nitrification assays with allylthiourea (ATU), dilute cultures exhibited more significant inhibition than concentrated cultures. So there were biomass-related effects; however, these differences minimally impacted the EC₅₀ values. Using different nutrient-media compositions had a minimal effect; however, switching mineral media for the toxicity test from the original cultivation media is not recommended because it reduced the original biomass nitrification capacity. Our results demonstrated that these factors substantially impact the performance of the nitrifying inoculum used in acute bioassays, and consequently, affect the response of AOB-NOB populations during the toxicant exposure. These are not highlighted in operation standards, and unfortunately, they can have significant consequential impacts on the determinations of toxicological endpoints. Moreover, the practical procedures tested here could support other authors in developing testing methodologies, adding quality checks in the experimental framework with minimal waste of time and resources.

Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata

The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.

Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants

Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH₄⁺ concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.

Ammonia- and Nitrite-Oxidizing Bacteria are Dominant in Nitrification of Maize Rhizosphere Soil Following Combined Application of Biochar and Chemical Fertilizer

Autotrophic nitrification is regulated by canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, most studies have focused on the role of canonical ammonia oxidizers in nitrification while neglecting the NOB. In order to understand the impacts of combined biochar and chemical fertilizer addition on nitrification and associated nitrifiers in plant rhizosphere soil, we collected rhizosphere soil from a maize field under four different treatments: no fertilization (CK), biochar (B), chemical nitrogen (N) + phosphorus (P) + potassium (K) fertilizers (NPK), and biochar + NPK fertilizers (B + NPK). The potential nitrification rate (PNR), community abundances, and structures of AOA, AOB, complete ammonia-oxidizing bacteria (Comammox Nitrospira clade A), and Nitrobacter- and Nitrospira-like NOB were measured. Biochar and/or NPK additions increased soil pH and nutrient contents in rhizosphere soil. B, NPK, and B + NPK treatments significantly stimulated PNR and abundances of AOB, Comammox, and Nitrobacter- and Nitrospira-like NOB, with the highest values observed in the B + NPK treatment. Pearson correlation and random forest analyses predicted more importance of AOB, Comammox Nitrospira clade A, and Nitrobacter- and Nitrospira-like NOB abundances over AOA on PNR. Biochar and/or NPK additions strongly altered whole nitrifying community structures. Redundancy analysis (RDA) showed that nitrifying community structures were significantly affected by pH and nutrient contents. This research shows that combined application of biochar and NPK fertilizer has a positive effect on improving soil nitrification by affecting communities of AOB and NOB in rhizosphere soil. These new revelations, especially as they related to understudied NOB, can be used to increase efficiency of agricultural land and resource management.

Nitratation in pilot-scale bioreactors fed with effluent from a submerged biological aerated filter used in the treatment of dog wastewater

Nitrification is a biochemical process that allows oxidation of ammonium ion to nitrite, and nitrite to nitrate in a system. Aerobic processes, such as use of submerged biological aerated filter (SBAF), enable nitrification. However, some variables that are entirely unavailable or not available at the required concentration range may hamper the process. In this study, nitratation under high dissolved oxygen (DO) concentrations was evaluated in laboratory-scale bioreactors containing 10% inoculum (0.5 kg kg^-1) fed with affluent from a SBAF that receive the sewage generated from washing the bays of a dog kennel. The following variables were monitored over time: ammoniacal nitrogen (12.44-29.62 mg L^-1), nitrite (0.28-0.54 mg L^-1), nitrate (1.75-3.55 mg L^-1), pH (8.11 ± 0.62), temperature (21.61 ± 1.24°C) and DO (9.69 ± 0.36 mg L^-1). Quantification of nitrifying bacteria by the multiple tube technique showed the value of 1.4 × 10¹² MPN mL^-1for ammonia-oxidizing bacteria (AOB) and 9.2 × 10¹⁴ MPN mL^-1 for nitrite-oxidizing bacteria. These values were higher than those found in a synthetic medium, which can be explained by the greater availability of ammonium and nitrite in the effluent. By the extraction of genomic DNA, and PCR, with specific primers, the presence of the AmoA (Ammonia monooxygenase) gene for AOB and of the Nitrobacter was detected in the bioreactor samples. By PCR-DGGE, the sequenced bands showed high similarity with denitrifying bacteria, such as Pseudomonas, Limnobacter, Thauera, Rhodococcus, and Thiobacillus. Thus, the saturation of dissolved oxygen in the system resulted in improvement in the nitratation step and allowed detection of bacterial genera involved in the process.

Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.

Dominance of comammox Nitrospira in soil nitrification

The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.

Short-term impact of fire on the total soil microbial and nitrifier communities in a wet savanna

Savannas are characterized by the coexistence of grasses and trees. Fires are critical for their coexistence, because they decrease the survival of tree seedlings and saplings and their recruitment to the adult stage. In some humid savannas, perennial grasses inhibit nitrification and trees stimulate nitrification, which likely favors coexistence between trees and grasses. However, fires may influence plant capacity to control nitrogen cycling, which could subsequently influence tree-grass coexistence and savanna nitrogen budget. Therefore, we sampled soil in a humid savanna of Ivory Coast under the dominant nitrification-inhibiting grass species and the dominant nitrification-stimulating tree species and under bare soil before and after (i.e., 5 days) fire during the long dry season. We quantified the total microbial and nitrifier abundances and transcriptional activities and the nitrification enzyme activity. Fire decreased soil water content, probably by increasing evaporation and, maybe, by triggering the growth of grasses, and increased soil ammonium availability likely due to ash deposition and increased mineralization. Fire did not impact the total archaeal, bacterial, or fungal abundances, or that of the nitrifiers. Fire did not impact archaeal transcriptional activity and increased bacterial and fungal total transcriptional activities. In contrast, fire decreased the archaeal nitrifier transcriptional activities and the nitrification enzymatic activity, likely due to the often reported resumption of the growth of nitrification-inhibiting grasses quickly after the fire (and the subsequent increase in root exudation). These results pave the way for a better understanding of the short-term effects of fire on nitrogen cycling and tree-grass competition for nitrogen.

Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization

Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Rapid achieving partial nitrification in domestic wastewater: Controlling aeration time to selectively enrich ammonium oxidizing bacteria (AOB) after simultaneously eliminating AOB and nitrite oxidizing bacteria (NOB)

This study developed a novel strategy for rapidly achieving partial nitrification (PN) without additional chemical agents, and infrastructure costs, only by controlling aeration time to selectively enrich ammonium oxidizing bacteria (AOB) after simultaneously eliminating AOB and nitrite oxidizing bacteria (NOB). Shorter aeration time and sludge retention time (10 days) were implemented to simultaneously eliminate AOB and NOB, the bioactivities drastically decreased to 13 and 0%, respectively. Subsequently, a gradually prolonged aeration time selectively enriched AOB and resulted in PN. The amoA abundances increased to 1.9 × 10¹⁰ copies gVSS^-1, whereas Nitrospira and Nitrobacter abundances remained stable (3.2 × 10⁹ and 3.1 × 10⁹ copies gVSS^-1). A nitrite accumulation rate above 96% was achieved and maintained for 205 days over the entire temperature range (28.5-17.9 °C). The effluent contained 1.9 mg N L^-1 of ammonium, 25.3 mg N L^-1 of nitrite, and less than 1.0 mg N L^-1 of nitrate, facilitating mainstream wastewater anammox.

Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils

The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg^-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg^-1), while the combined toxicity of high-concentration SDZ (10 mg · kg^-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg^-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg^-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg^-1 Cu combined with 5 mg · kg^-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.

The long-term effects of using nitrite and urea on the enrichment of comammox bacteria

The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tolerance, which could only be found in several ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This implies that using nitrite and urea as nitrogen sources may accelerate comammox bacteria's enrichment efficiency. In this study, two reactors using nitrite and urea as substrates, respectively, were operated for 390 days. At the end of cultivation, the reactor fed with urea exhibited higher nitrification potential than the reactor fed with nitrite. Comammox bacteria outcompeted AOA and AOB, regardless of whether they were cultured with nitrite or urea. Using nitrite can improve the proportion of comammox amoA to total amoA of 92%, while using urea may increase the proportion of comammox bacteria among total bacteria to 14.2%. Metagenomic results implied that nitrite was converted to ammonia by nitrate reduction and absorbed by comammox bacteria. On the other hand, urea may be directly utilized as substrate. These results demonstrated that using different nitrogen sources caused niche differentiation of comammox bacteria, AOA, and AOB. Using nitrite can increase the relative abundance of comammox amoA to total amoA, while using urea can increase the quantity of comammox amoA. Comammox bacteria were dominant among ammonia oxidizing microorganisms for both nitrite and urea cultures.

The effect of the COD: N ratio on mainstream deammonification in an integrated fixed-film activated sludge sequencing batch reactor

For eight months, a sequencing batch reactor (SBR) with integrated fixed-film activated sludge (IFAS) was operated in ambient temperature to study engineering and practical aspects of application of deammonification for mainstream conditions. For biofilm formation, K3 Kaldnes carriers were used, where the anaerobic ammonium oxidation (anammox) process can occur in deep layers of biofilm, while partial nitritation occurs in oxygen-rich outer layers. After the initial running phase of the reactor (Phase 1) to provide time for microorganisms to adapt, the COD: N ratio increased to around 2.6 in Phase 2 through reducing the ammonium concentration and increasing COD in synthetic wastewater to get closer to mainstream conditions. The total reaction time in each half-day batch cycle was kept 625 min throughout various phases, but the duration of intermittent aeration was regulated at 4 ± 1 min. While final nitrogen removal efficiency (NRE) for Phase 1 was 43%, at the end of Phase 2, it decreased to 37%. However, a maximum NRE at 90% was achieved during Phase 2. The identification of the responsible microorganisms was made through Fluorescence in situ hybridization (FISH), while Mixed Liquor Suspended Solid (MLSS) and Mixed Liquor Volatile Suspended Solid (MLVSS) was used to estimate the physical presence of bacteria. Ammonium oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AnAOB) were dominant bacteria, respectively. The adverse effects of a gradual increase of COD: N ratio from 0.17 to more than 2.0 caused a decline in NRE to around 15%.

Do soil property variations affect dicyandiamide efficiency in inhibiting nitrification and minimizing carbon dioxide emissions?

Nitrification inhibitors (NIs) are used to retard the nitrification process and reduce nitrogen (N) losses. However, the effects of soil properties on NI efficacy are less clear. Moreover, the direct and indirect effects of soil property variations on NI efficiency in minimizing carbon dioxide (CO₂) emissions have not been previously studied. An incubation experiment was conducted for 40 days with two treatments, N (200 mg N-urea kg^-1) and N + dicyandiamide (DCD) (20 mg DCD kg^-1), and a control group (without the N) to investigate the response of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to DCD application and the consequences for CO₂, nitrous oxide (N₂O) and ammonia (NH₃) emissions from six soils from the Loess Plateau with different properties. The nitrification process completed within 6-18 days for the N treatment and within 30->40 days for the N + DCD treatment. AOB increased significantly with N fertilizer application, while this effect was inhibited in soils when DCD was applied. AOA was not sensitive to N fertilizer and DCD application. The nitrification rate was positively correlated with the clay (p < 0.05) and SOM contents (p < 0.01); DCD was more effective in loam soil with low SOM and high soil pH. Soil pH significantly was decreased with N fertilizer application, while it increased when DCD was applied. Moreover, DCD application decreased CO₂ emissions from soils by 22%-172%; CO₂ emissions were negatively correlated with the clay and SOM contents. DCD application decreased N₂O emissions in each soil by 1.0- to 94-fold compared with those after N fertilizer application. In contrast, DCD application increased NH₃ release from soils by 59-278%. NH₃ volatilization was negatively correlated with clay (p < 0.05) and SOM (p < 0.01) contents and positively correlated with soil pH (p < 0.01). Therefore, soil texture, SOM and soil pH have significant effects on the DCD performance, nitrification process and gaseous emissions.

Effective nitrogen removal from ammonium-depleted wastewater by partial nitritation and anammox immobilized in granular and thin layer gel carriers

This study investigates the effect of physicochemical conditions on the partial nitritation and anammox treatment by immobilized ammonia oxidizers under ammonium-deplete conditions. The impact of oxygen and temperature was studied by measuring the activity of immobilized aerobic and anaerobic ammonia-oxidizing organisms (Ammonia-oxidizing bacteria (AOB) and archaea (AOA), and Anammox bacteria) embedded in polyvinyl alcohol - sodium alginate (PVA-SA) beads and in thin layer poly-ethylene glycol hydrogels. Beads and flat hydrogels were incubated in a fluidized bed reactor (FBR) and in two flow cells, respectively. Both systems were fed with synthetic wastewater (15 mg N-NH₄⁺/L) at different temperatures (20 °C and/or 30 °C) and different dissolved oxygen (DO) concentrations (0.1, 0.3, 0.5 and/or 1 mg/L) over 152 and 207 days, respectively. The FBR system had a maximum removal rate of 1.7 g-N/m³/d at 0.1 mg O₂/L, corresponding to 80% removal efficiency, while a high aerobic ammonia-oxidizing activity but a partial oxygen inhibition of Anammox bacteria were observed at higher DO concentrations. In both flow cells, nitrogen removal efficiency was highest (80%) at 30 °C and 1 mg O₂/L while removal was less favorable at lower DO and lower temperature. Our results indicate a potential use of hydrogel beads for an energy efficient technology with reduced aeration demand for treating low ammonia wastewater, while layered hydrogels are a possible first step for biological treatments of wastewater using tangential flow. In addition, we provide blueprint drawings of the flow cells, which may be used to 3D-print the apparatus for other applications.

Newly designed high-coverage degenerate primers for nitrogen removal mechanism analysis in a partial nitrification-anammox (PN/A) process

Reliable tools for quantification of different functional populations are required to achieve stable, effective nutrients removal in partial nitrification and anammox (PN/A) processes. Here we report the design and validation of degenerate PCR primer pairs targeting anammox bacteria, aerobic ammonium-oxidizing bacteria (AeAOB) and nitrite-oxidizing bacteria (NOB) with high coverage but without sacrificing specificity. The new primer pairs are able to cover a broader range of the targeted populations (58.4 vs 21.7%, 49.5 vs 47.6%, 80.7 vs 57.2% and 70.5 vs 42.3% of anammox bacteria, AeAOB, Nitrobacter and Nitrospina, respectively) than previously published primers. Particularly, the Amx719F/875R primer can retrieve a larger number of 16S rRNA genes from different types of samples with amplicons covering all known anammox bacteria genera (100% coverage) including the recently found novel genus, Asahi BRW. These newly desinged primers will provide a more reliable molecular tool to investigate the mechanisms of nitrogen removal in PN/A processes, which can provide clearer links between reactor performance, the metabolic activities and abundances of functional populations, shedding light on conditions that are favorable to the establishment of stable PN/A.

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)

Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH₄⁺) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R² = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH₄⁺ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.

Recovering partial nitritation in a PN/A system during mainstream wastewater treatment by reviving AOB activity after thoroughly inhibiting AOB and NOB with free nitrous acid

Starting up or recovering partial nitritation is a major challenge for achieving or maintaining stable partial nitritation/anammox (PN/A) during mainstream wastewater treatment. This study presents a novel strategy for recovering the nitrite pathway by selectively reviving ammonium oxidizing bacteria (AOB) after thoroughly inhibiting AOB and nitrite oxidizing bacteria (NOB) using free nitrous acid (FNA). A sequencing batch reactor was operated for PN/A to treat real domestic wastewater for 423 days, during which twice FNA treatment was temporarily implemented. Results showed that with a single 0.45 mg/L FNA treatment on flocculent sludge, the NO₃^--N concentration during the aerobic period showed an uptrend again and the partial nitritation performance was deteriorated. In contrast, 1.35 mg/L FNA treatment induced the inhibition of both AOB and NOB leading to regressive ammonium oxidation, but a subsequently higher DO (1.5 mg/L) and longer aeration duration recovered partial nitritation. For the relative abundances of the acquired biomass related to nitrogen conversion, Nitrosomonas, Nitrospira and Nitrolancea increased to 9.65%, 10.27% and 4.35%, respectively, at the beginning of the 1.35 mg/L FNA treatment, and Nitrospira and Nitrolancea decreased to 2.80% and 0.03% whereas Nitrosomonas declined to 8.71% after 76 days. Ca. Brocadia showed less resilience after the 1.35 mg/L FNA treatment, with the relative abundance decreasing from 13.38% to 0.62% due to insufficient nitrite. Molecular ecological network analysis indicates that among anammox taxa, Ca. Kuenenia and Ca. Brocadia formed important links with other N cycle processes. Moreover, the proposed strategy shows operational flexibility because it can be easily used to control NOB in mainstream PN/A applications offered by flocculent sludge systems.

Biogeographic distribution of comammox bacteria in diverse terrestrial habitats

Comammox, the microbial group capable of completely oxidizing ammonia to nitrate, challenged the traditional two-step nitrification process where ammonia is oxidized by ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite by nitrite-oxidizing bacteria (NOB). However, the distribution of comammox bacteria in various habitats and their potential environmental drivers remain poorly understood. Using qPCR and high-throughput sequencing approach, we analyzed the abundance and community patterns of comammox from 38 samples taken from five different habitat types including paddy fields in Shaoguan and Antu, the wheat fields, river, and grassland in the Qinghai-Tibet Plateau, and the fringe and central riparian zones of Chaohu Lake of China during winter and summer. Comammox bacteria were detected in all samples, with Ca. N. nitrificans dominating the community, followed by Ca. N. nitrosa. Generally, in paddy fields of Shaoguan and Antu, ammonia (NH₄⁺) was the key factor affecting comammox bacteria. However, in wheat fields, river and grassland of the Qinghai-Tibet Plateau, altitude was the strongest factor affecting comammox bacteria. In Chaohu Lake, comammox bacteria showed temporal heterogeneity, being higher in winter than summer, especially in the fringe riparian zone. Our results suggest that comammox is widespread in diverse habitats and exhibit niche partitioning, and can be affected by different environmental factors that may vary by habitat.

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.

Using digital polymerase chain reaction to characterize microbial communities in wetland mesocosm soils under different vegetation and seasonal nutrient loadings

Constructed wetlands are multi-functional systems that can effectively store and transform pollutants primarily through natural processes. However, the removal of nitrogen pollutant by wetlands is highly variable, likely due to a combination of factors such as plant species-specific assimilation behavior, the effects of soil microbial diversity, and variable nitrogen inputs. In this study, the effects of plant species richness (i.e., number of plant species in a system) and seasonal nutrient loading (i.e., nitrogen fertilization) on the microbial community responsible for regulating nitrogen turnover in wetland mesocosm soils was investigated. Digital polymerase chain reaction was used to quantify bacterial abundance. Principal component analysis was employed to identify dominant patterns within the data, and resampling-based analysis of variance was used to assess statistical significance of any observed differences caused by fertilization, season, and/or plant species richness. Results indicated that fertilization or season, which was convolved with fertilization, was the dominant factor influencing the microbial community in the study environment. The effects of plant species richness were more nuanced. Its greater richness significantly impacted the abundance of only a subset of bacterial groups (i.e., the ammonia oxidizing bacteria, Nitrospira spp. of nitrite-oxidizing bacteria, and comammox, but not the denitrifying bacteria).

Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil

This study intended to evaluate the combined effects of both biochar and organic fertilizer on nitrous oxide (N₂O) fluxes and composition of nitrifier and denitrifier of saline-alkali soil. Therefore, four different treatments such as CK (only chemical fertilizer), B (only biochar), M (only organic fertilizer), BM (B:M = 1:1) were used in this experiment. The results showed that N₂O emissions were decreased in B and BM treatments compare to the control. In contrast, N₂O emissions were highest before day 12 but lowest after day 19 in M treatment compare to the control. Application of biochar, organic fertilizer and biochar plus organic fertilizer decreased the nirS and nirK genes copies and enhanced the nosZ gene copies which resulting in the lower N₂O fluxes. The ammonia-oxidizing bacteria (AOB) amoA and nirK genes copies were significantly increased by organic fertilizer before day 12, leading to high N₂O emissions. The genera Nitrosospira (AOB) and Nitrososphaera (ammonia-oxidizing archaea, AOA) assumed absolute superiority. Additionally, Nitrosospira (AOB) was also appeared in nirK-type denitrifiers, illustrating denitrification was carried out by nitrifiers. The genera Azospirillum (nirS), Burkholderia (nosZ) and Polymorphum (nosZ) were dominant in CK. There was only one dominant genus, Mesorhizobium (nosZ) in the B treatment. The genera Mesorhizobium (nirK), Azoarcus (nirS), Kocuria (nirS) and Pseudomonas (nosZ) occupied the main status in the M treatment. The relative abundance of Rhodanobacter (nirS) and Azospirillum (nosZ) were higher in the BM treatment compared with other treatments. Soil water content (SWC), pH, NH₄⁺-N and NO₃^--N were the main factors affecting AOB and denitrifiers, which influencing N₂O emissions. Overall, combined application of biochar and organic fertilizer can reduce the N₂O emission where AOB and nirK-type denitrifier were the main contributors to the N₂O emission.

Furan formation from ingredient interactions and furan mitigation by sugar alcohols and antioxidants of bamboo leaves in milk beverage model systems

BACKGROUND

Furan is a potential carcinogen that can be formed in various heat-treated foods, including milk beverages. Studies on the formation and mitigation of furan in milk beverages are rare. In the present study, the effects of ingredients on furan formation and the reduction of furan by sugar alcohols and antioxidants of bamboo leaves (AOB) were investigated in a milk beverage model system.

RESULTS

The results obtained demonstrated that the Maillard reaction is the major pathway for furan formation in a milk beverage model system, and the type of sugar has a great influence on furan formation. High fructose corn syrup (HFCS 55) was more favorable for furan formation than sucrose. Thermal oxidation of ascorbic acid and lipids significantly enhanced furan generation. Xylitol, sorbitol and mannitol inhibited furan formation in model systems by replacing sucrose or HFCS. The maximum inhibition percentage of furan formation was observed when sucrose/HFCS was substituted completely by xylitol and the inhibition rate was 78.28% and 88.64% separately for the sucrose/HFCS-containing system. AOB significantly inhibited furan formation and the inhibition rate reached 32.13% and 28.52% separately for the sucrose/HFCS-containing system.

CONCLUSION

The present study demonstrates that the use of sugar alcohols and AOB could be a feasible way of reducing furan formation in thermally processed milk beverages. © 2019 Society of Chemical Industry.

Does the feeding strategy enhance the aerobic granular sludge stability treating saline effluents?

The development and stability of aerobic granular sludge (AGS) was studied in two Sequencing Batch Reactors (SBRs) treating fish canning wastewater. R1 cycle comprised a fully aerobic reaction phase, while R2 cycle included a plug-flow anaerobic feeding/reaction followed by an aerobic reaction phase. The performance of the AGS reactors was compared treating the same effluents with variable salt concentrations (4.97-13.45 g NaCl/L) and organic loading rates (OLR, 1.80-6.65 kg CODs/(m³·d)). Granulation process was faster in R2 (day 34) than in R1 (day 90), however the granular biomass formed in the fully aerobic configuration was more stable to the variable feeding composition. Thus, in R1 solid retention times (SRT), up to 15.2 days, longer than in R2, up to 5.8 days, were achieved. These long SRTs values helped the retention of nitrifying organisms and provoked the increase of the nitrogen removal efficiency to 80% in R1 while it was approximately of 40% in R2. However, the presence of an anaerobic feeding/reaction phase increased the organic matter removal efficiency in R2 (80-90%) which was higher than in R1 with a fully aerobic phase (75-85%). Furthermore, in R2 glycogen-accumulating organisms (GAOs) dominated inside the granules instead of phosphorous-accumulating organisms (PAOs), suggesting that GAOs resist better the stressful conditions of a variable and high-saline influent. In terms of AGS properties an anaerobic feeding/reaction phase is not beneficial, however it enables the production of a better quality effluent.

A novel process of the isolation of nitrifying bacteria and their development in two different natural lab-scale packed-bed bioreactors for trichloroethylene bioremediation

Trichloroethylene (TCE) is a carcinogenic compound that is commonly present in groundwater and has been detected in drinking water sources for Mexican towns in the Mexico-US border area. Nitrifying bacteria, such as Nitrosomonas europaea, have been shown to be capable of degrading halogenated compounds, including TCE, but it is difficult to obtain high cell concentrations of these bacteria. The aim of the present study was to generate biomass of a nitrifying bacterial consortium from the sludge of an urban wastewater treatment plant (WWTP) and evaluate its capacity to biodegrade TCE in two different natural lab-scaled packed bed bioreactors. The consortium was isolated by a novel method using a continuous stirred-tank bioreactor inoculated with activated sludge from the Domos WWTP located in Cd. Obregón, Sonora, Mexico. The bioreactor was fed with specific media to cultivate ammonia-oxidizing bacteria at a dilution rate near the maximum specific growth rate reported for Nitrosomonas europaea. Optical density and suspended solids measurements were performed to determine the culture biomass production, and the presence of inorganic nitrogen species was determined by spectrophotometry. The presence of nitrifying ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was confirmed by PCR amplification, and biofilm formation was observed by scanning electron microscopy. Batch-scale experiments confirmed the biodegradative activity of the isolated consortium, which was subsequently fixed in an inorganic carrier as zeolite and a synthetic carrier such as polyurethane to both be used as lab-scale packed-bed bioreactors, with up to 58.63% and 62.7% of TCE biodegradation achieved, respectively, demonstrating a possible alternative for TCE bioremediation in environmental and engineering systems.

Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling

The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0-675 kg N ha^-1 year^-1), phosphorus (0-405 kg P₂O₅ ha^-1 year^-1), and potassium (0-675 kg K₂O ha^-1 year^-1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB-amoA gene abundance, while AOA were not as sensitive as AOB. The comammox-amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox-amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils.

Successful operation performance and syntrophic micro-granule in partial nitritation and anammox reactor treating low-strength ammonia wastewater

The stable operation of the partial nitritation and anammox (PN/A) process is a challenge in the treatment of low-strength ammonia wastewater like sewage mainstream. This study demonstrated the feasibility of achieving stable operation in the treatment of 50 mg/L ammonia wastewater with a micro granule-based PN/A reactor. The long-term operation results showed nitrogen removal efficiencies of 71.8 ± 9.9% were stably obtained under a relatively short hydraulic retention time (HRT) of 2 h. The analysis on the physicochemical properties of the granules indicated most of the granules were in a size in a range of 265-536 μm, and the elementary composition of the granules was determined to be CH_1.61O_0.61N_0.17S_0.01P_0.03. The microbial analysis revealed Candidatus Kuenenia stuttgartiensis anammox bacteria and Nitrosomonas-like AOB were the two most dominant bacteria with 27.6% and 10.5% abundance, respectively, both of which formed spatially syntrophic co-immobilization within the micro-granules. The ex-situ activity tests showed the activity of NOB was well limited through DO regulation in the reactor. These results provide an alternative PN/A process configuration for low-strength wastewater treatment by sustaining microstate granules. Optimization of the nitrogen sludge loading rate and DO regulation are important for the successful performance.

Free nitrous acid (FNA) induced transformation of sulfamethoxazole in the enriched nitrifying culture

The sulfonamide antibiotics sulfamethoxazole (SMX) has been frequently detected in the wastewater. It has been reported that part of SMX can be transformed by the co-metabolism of ammonia oxidizing bacteria (AOB) during nitrifying process. However, previous studies reported inconsistent or even contradictory results in terms of SMX degradation and/or transformation. Literature study revealed that nitrite may play certain role in SMX transformation, which has been neglected previously. In this study, the transformation behavior of SMX was investigated with and without the presence of nitrite in an enriched nitrifying culture. The results clearly show that the elimination of SMX occurred with the presence/accumulation of nitrite, and a linear regression was observed between SMX elimination efficiency and free nitrous acid (FNA) concentration, indicating that FNA was the major factor responsible for the SMX transformation. By reacting with FNA, SMX transformation products, such as 4-nitro-SMX, desamino-SMX and hydroxylated SMX, were detected. However, when FNA concentration decreased, these intermediates may be retransformed back to SMX. These findings improved our understanding on SMX transformation in a biological system and highlighted the role of nitrite/FNA in the sulfonamide antibiotics degradation.

Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave

The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.