Impact of additives on syntrophic propionate and acetate enrichments under high-ammonia conditions.

High ammonia concentrations in anaerobic degradation systems cause volatile fatty acid accumulation and reduced methane yield, which often derive from restricted activity of syntrophic acid-oxidising bacteria and hydrogenotrophic methanogens. Inclusion of additives that facilitate the electron transfer or increase cell proximity of syntrophic species by flocculation can be a suitable strategy to counteract these problems, but its actual impact on syntrophic interactions has yet to be determined. In this study, microbial cultivation and molecular and microscopic analysis were performed to evaluate the impact of conductive (graphene, iron oxide) and non-conductive (zeolite) additives on the degradation rate of acetate and propionate to methane by highly enriched ammonia-tolerant syntrophic cultures derived from a biogas process. All additives had a low impact on the lag phase but resulted in a higher rate of acetate (except graphene) and propionate degradation. The syntrophic bacteria 'Candidatus Syntrophopropionicum ammoniitolerans', Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen were found in higher relative abundance and higher gene copy numbers in flocculating communities than in planktonic communities in the cultures, indicating benefits to syntrophs of living in close proximity to their cooperating partner. Microscopy and element analysis showed precipitation of phosphates and biofilm formation in all batches except on the graphene batches, possibly enhancing the rate of acetate and propionate degradation. Overall, the concordance of responses observed in both acetate- and propionate-fed cultures highlight the suitability of the addition of iron oxide or zeolites to enhance acid conversion to methane in high-ammonia biogas processes. KEY POINTS: • All additives promoted acetate (except graphene) and propionate degradation. • A preference for floc formation by ammonia-tolerant syntrophs was revealed. • Microbes colonised the surfaces of iron oxide and zeolite, but not graphene.

Novel therapeutic targets: bifidobacterium-mediated urea cycle regulation in colorectal cancer.

BACKGROUND AND PURPOSE: Colorectal cancer (CRC) is a widespread malignancy with a complex and not entirely elucidated pathogenesis. This study aims to explore the role of Bifidobacterium in the urea cycle (UC) and its influence on the progression of CRC, a topic not extensively studied previously. EXPERIMENTAL APPROACH: Utilizing both bioinformatics and experimental methodologies, this research involved analyzing bacterial abundance in CRC patients in comparison to healthy individuals. The study particularly focused on the abundance of BA. Additionally, transcriptomic data analysis and cellular experiments were conducted to investigate the impact of Bifidobacterium on ammonia metabolism and mitochondrial function, specifically examining its regulation of the key UC gene, ALB. KEY RESULTS: The analysis revealed a significant decrease in Bifidobacterium abundance in CRC patients. Furthermore, Bifidobacterium was found to suppress ammonia metabolism and induce mitochondrial dysfunction through the regulation of the ALB gene, which is essential in the context of UC. These impacts contributed to the suppression of CRC cell proliferation, a finding corroborated by animal experimental results. CONCLUSIONS AND IMPLICATIONS: This study elucidates the molecular mechanism by which Bifidobacterium impacts CRC progression, highlighting its role in regulating key metabolic pathways. These findings provide potential targets for novel therapeutic strategies in CRC treatment, emphasizing the importance of microbiota in cancer progression.

Synergistic effect and microbial community structure of waste-activated sludge and kitchen waste solids residue mesophilic anaerobic co-digestion.

Anaerobic co-digestion was conducted on the solid residues after three-phase separation of kitchen waste (KWS) and waste-activated sludge (WAS), the synergistic effects and process performance were studied during co-digestion at different ratios of KWS to WAS. KWS and WAS mix ratios of 0:1, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1 and 1:0 (based on TS). The results showed that a ratio of KWS to WAS of 1:1 got a very high methane recovery with a methane yield of 310.45 ± 30.05 mL/g VSadded. The highest concentration of free ammonia among all reaction systems was only 70.23 ± 5.53 mg/L, which was not enough to produce ammonia inhibition in the anaerobic co-digestion system. However, when the KWS content exceeded 50%, methane inhibition and prolongation of the lag phase were observed due to the accumulation of volatile fatty acids (VFAs), and during the lag phase. Microbial community analysis showed that various bacterial groups involved in acid production and hydrolysis were mainly dominated by phylum Firmicutes, Chloroflexi, Proteobacteria and Bacteroidetes. Hydrogenotrophic methanogen was found to dominate all archaeal communities in the digesters. Co-digestion of KWS with WAS significantly increased the relative abundance of Methanobacterium compared with anaerobic digestion of WAS alone.

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome.

The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long-reads located within the flexible genomic islands (fGIs) identified by their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third-generation sequencing metagenomics.

Diverse metabolism drives comammox in continental-scale agricultural streams: Important ammonia oxidation but low N2O production.

Agriculture receives approximately 25 % of the annual global nitrogen input, 37 % of which subsequently runs off into adjacent low-order streams and surface water, where it may contribute to high nitrification and nitrous oxide (N2O). However, the mechanisms of nitrification and the pathways controlling N2O production in agricultural streams remain unknown. Here, we report that the third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is widespread and contributes to important ammonia oxidation with low ammonia-N2O conversion in both basin- and continental-scale agricultural streams. The contribution of comammox to ammonia oxidation (21.5 ± 2.3 %) was between that of bacterial (68.6 ± 2.7 %) and archaeal (9.9 ± 1.8 %) ammonia oxidation. Interestingly, N2O production by comammox (18.5 ± 2.1 %) was higher than archaeal (10.5 ± 1.9 %) but significantly lower than bacterial (70.2 ± 2.6 %) ammonia oxidation. The first metagenome-assembled genome (MAG) of comammox bacteria from agricultural streams further revealed their potential extensive diverse and specific metabolism. Their wide habitats might be attributed to the diverse metabolism, i.e. harboring the functional gene of nitrate reduction to ammonia, while the lower N2O would be attributed to their lacking biological function to produce N2O. Our results highlight the importance of widespread comammox in agricultural streams, both for the fate of ammonia fertilizer and for climate change. However, it has not yet been routinely included in Earth system models and IPCC global assessments. Synopsis Widespread but overlooked comammox contributes to important ammonia oxidation but low N2O production, which were proved by the first comammox MAG found in agricultural streams.

Hyphae of the fungus Aspergillus nidulans demonstrate chemotropism to nutrients and pH.

The importance of fungi in ecological systems and pathogenicity hinges on their ability to search for nutrients, substrates, and hosts. Despite this, the question of whether fungal hyphae exhibit chemotropism toward them remains largely unresolved and requires close examination at the cellular level. Here, we designed a microfluidic device to assess hyphal chemotropism of Aspergillus nidulans in response to carbon and nitrogen sources, as well as pH. Within this device, hyphae could determine their growth direction in a two-layer flow with distinct compositions that were adjacent but non-mixing. Under conditions with and without a carbon source, hyphae changed growth direction to remain in the presence of a carbon source, but it was still difficult to distinguish between differences in growth and chemotropism. Although nitrogen sources such as ammonia and nitrate are important for growth, the hyphae indicated negative chemotropism to avoid them depending on the specific transporters. This fungus grows equally well at the colony level in the pH range of 4 to 9, but the hyphae exhibited chemotropism to acidic pH. The proton pump PmaA is vital for the chemotropism to acid pH, while the master regulatory for pH adaptation PacC is not involved, suggesting that chemotropism and adaptive growth via gene expression regulation are distinct regulatory mechanisms. Despite various plasma membrane transporters are distributed across membranes except at the hyphal tip, the control of growth direction occurs at the tip. Finally, we explored the mechanisms linking these two phenomena, tip growth and chemotropism.

Performances of full-scale biological nitrogen pre-treatment process for drinking water source: Seasonal variations and microbial community.

This study investigated the performance of the full-scale unit over a two-year period to enhance nitrification efficiency and provide operational strategies. Results indicated that raw water quality from Donggan River was notably influenced by seasonal variations, particularly during dry and wet seasons, impacting the nitrification efficiency of the biological pretreatment process. Factors such as influent concentrations of ammonia and total Kjeldahl nitrogen were found to have significant effects on nitrification, with temperature and conductivity also showing correlations. The specific rate of ammonia removal was calculated to be approximately 0.1 kg-N/m3/d under the existing operational setup. Moreover, elevating dissolved oxygen levels above 4 mg/L was proposed to potentially boost ammonia oxidation based on findings from experiments conducted in lab-scale bioreactors. In times of increased influent ammonia levels, the elimination of about 1-3 mg-N/L of total nitrogen signified the activation of denitrification processes. This observation was corroborated by results from next-generation sequencing techniques, verifying the existence of denitrifying microorganisms. The real-time PCR analysis results indicated that the abundance of comammox amoA gene was comparable with the abundance of the AOB amoA gene, indicating the presence of comammox Nitrospira and their potential role on nitrification in the system.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies.

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation.

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Coordination of elemental sulfur and organic carbon source stimulates simultaneous nitrification and denitrification toward low C/N ratio wastewater.

The feasibility of inducing simultaneous nitrification and denitrification (SND) by S0 for low carbon to nitrogen (C/N) ratio wastewater remediation was investigated. Compared with S0 and/or organics absent systems (-3.4 %∼5.0 %), the higher nitrogen removal performance (18.2 %∼59.8 %) was achieved with C/N ratios and S0 dosages increasing when S0 and organics added simultaneously. The synergistic effect of S0 and organics stimulated extracellular polymeric substances secretion and weakened intermolecular binding force of S0, facilitating S0 bio-utilization and reducing the external organics requirement. It also promoted microbial metabolism (0.16 âˆ¼ 0.24 µg O2/(g VSS·h)) and ammonia assimilation (5.9 %∼20.5 %), thereby enhancing the capture of organics and providing more electron donors for SND. Furthermore, aerobic denitrifiers (15.91 %∼27.45 %) and aerobic denitrifying (napA and nirS) and ammonia assimilating genes were accumulated by this synergistic effect. This study revealed the mechanism of SND induced by coordination of S0 and organics and provided an innovative strategy for triggering efficient and stable SND.

Ammonia transporter RhBG initiates downstream signaling and functional responses by activating NFκB.

Transceptors, solute transporters that facilitate intracellular entry of molecules and also initiate intracellular signaling events, have been primarily studied in lower-order species. Ammonia, a cytotoxic endogenous metabolite, is converted to urea in hepatocytes for urinary excretion in mammals. During hyperammonemia, when hepatic metabolism is impaired, nonureagenic ammonia disposal occurs primarily in skeletal muscle. Increased ammonia uptake in skeletal muscle is mediated by a membrane-bound, 12 transmembrane domain solute transporter, Rhesus blood group-associated B glycoprotein (RhBG). We show that in addition to its transport function, RhBG interacts with myeloid differentiation primary response-88 (MyD88) to initiate an intracellular signaling cascade that culminates in activation of NFκB. We also show that ammonia-induced MyD88 signaling is independent of the canonical toll-like receptor-initiated mechanism of MyD88-dependent NFκB activation. In silico, in vitro, and in situ experiments show that the conserved cytosolic J-domain of the RhBG protein interacts with the Toll-interleukin-1 receptor (TIR) domain of MyD88. In skeletal muscle from human patients, human-induced pluripotent stem cell-derived myotubes, and myobundles show an interaction of RhBG-MyD88 during hyperammonemia. Using complementary experimental and multiomics analyses in murine myotubes and mice with muscle-specific RhBG or MyD88 deletion, we show that the RhBG-MyD88 interaction is essential for the activation of NFkB but not ammonia transport. Our studies show a paradigm of substrate-dependent regulation of transceptor function with the potential for modulation of cellular responses in mammalian systems by decoupling transport and signaling functions of transceptors.

Response and recovery of nitrifying moving bed biofilm reactor systems exposed to 1°C with varying levels of ammonia starvation.

This study investigated the impact of varying total ammonia nitrogen (TAN) feed levels along with water temperature decreases on the performance of nitrifying moving bed biofilm reactor (MBBR) at 1 °C and its recovery at 3 °C. Five MBBR reactors were operated with different TAN concentrations as water temperature decreased from 20 to 3 °C: reactor R1 at 30 mg N/L, reactor R2 at 20 mg N/L, reactor R3 at 15 mg N/L, reactor R4 at 10 mg N/L and reactor R5 at 0 mg N/L. The corresponding biofilm characteristics were also analyzed to understand further nitrifying MBBR under different TAN feeding scenarios. The findings revealed that the higher TAN levels were before reaching 1 °C, the better nitrification performance and the more biomass grew. However, the highest TAN concentration (30 mg N/L) might negatively affect the nitrification performance, the activity of nitrifiers, and the growth of biofilms at 1 °C because of the toxic effects of un-ionized or free ammonia (FA). It was observed that the activities of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were affected by FA concentrations ranging from 0.2 to 0.7 mg N/L at 1 °C, but they could gradually be adapted to such inhibitory environment, with NOB recovering more quickly and robustly than AOB. The study identified 20 mg N/L (67 % of maximum influent TAN at 1 °C in R2 as the optimal TAN feeding concentration, achieving over 90 % TAN removal and a surface area removal rate (SARR) of 0.78 ± 0.02 g N/m2·d at 1 °C. Meanwhile, R2 also exhibited the highest biofilm mass, with total solids at 13.3 mg/carrier and volatile solids at 11.3 mg/carrier. As TAN was removed, nitrite accumulation was observed at 1 °C, and higher influent TAN concentrations prior to 1 °C appeared to delay the accumulation. When water temperature increased from 1 °C to 3 °C, nitrification performance improved significantly in all reactors without nitrite accumulation, and the higher TAN feeding in the previous stage led to faster recovery. Compared with 20 °C, biofilm became thinner and denser at 1 °C and 3 °C. Furthermore, this study revealed significant shifts in microbial community composition and nitrifier abundances in response to changes in water temperature and influent TAN levels. The dominant nitrifiers were identified as Nitrosomonadaceae (AOB) and Nitrospiraceae (NOB). At 1 °C, the nitrifier abundances were significantly correlated with SARRs, FA, and biofilm density. R2, which exhibited the best nitrification performance, maintained higher nitrifier abundances at 1 °C.

Significant in situ sludge yield reduction in an acidic activated sludge system.

Minimizing sludge generation in activated sludge systems is critical to reducing the operational cost of wastewater treatment plants (WWTPs), particularly for small plants where bioenergy is not recovered. This study introduces a novel acidic activated sludge technology for in situ sludge yield reduction, leveraging acid-tolerant ammonia-oxidizing bacteria (Candidatus Nitrosoglobus). The observed sludge yield (Yobs) was calculated based on the cumulative sludge generation and COD removal during 400 d long-term operation. The acidic process achieved a low Yobs of 0.106 ± 0.004 gMLSS/gCOD at pH 4.6 to 4.8 and in situ free nitrous acid (FNA) of 1 to 3 mg/L, reducing sludge production by 58 % compared to the conventional neutral-pH system (Yobs of 0.250 ± 0.003 gMLSS/gCOD). The acidic system also maintained effective sludge settling and organic matter removal over long-term operation. Mechanism studies revealed that the acidic sludge displayed higher endogenous respiration, sludge hydrolysis rates, and higher soluble microbial products and loosely-bounded extracellular polymer substances, compared to the neutral sludge. It also selectively enriched several hydrolytic genera (e.g., Chryseobacterium, Acidovorax, and Ottowia). Those results indicate that the acidic pH and in situ FNA enhanced sludge disintegration, hydrolysis, and cryptic growth. Besides, a lower intracellular ATP content was observed for acidic sludge than neutral sludge, suggesting potential decoupling of catabolism and anabolism in the acidic sludge. These findings collectively demonstrate that the acidic activated sludge technology could significantly reduce sludge yield, contributing to more cost- and space-effective wastewater management.

Mechanistic insight into microbial interaction and metabolic pattern of anammox consortia on surface-modified biofilm carrier with extracellular polymeric substances.

The extremely slow growth rate of anaerobic ammonia oxidation (anammox) bacteria limits full-scale application of anammox process worldwide. In this study, extracellular polymeric substances (EPS)-coated polypropylene (PP) carriers were prepared for biofilm formation. The biomass adhesion rate of EPS-PP carrier was 12 times that of PP carrier, and EPS-PP achieved significant enrichment of E. coli BY63. The 120-day continuous flow experiment showed that the EPS-PP carrier accelerated the formation of anammox biofilm, and the nitrogen removal efficiency increased by 10.5 %. In addition, the abundance of Candidatus Kuenenia in EPS-PP biofilm was 27.1%. Simultaneously, amino acids with high synthesis cost and the metabolites of glycerophospholipids related to biofilm formation on EPS-PP biofilm were significantly up-regulated. Therefore, EPS-PP carriers facilitated the rapid formation of anammox biofilm and promoted the metabolic activity of functional bacteria, which further contributed to the environmental and economic sustainability of anammox process.

Increasing urine nitrification performance with sequential membrane aerated biofilm reactors.

This study aimed to investigate whether separating organics depletion from nitrification increases the overall performance of urine nitrification. Separate organics depletion was facilitated with membrane aerated biofilm reactors (MABRs). The high pH and ammonia concentration in stored urine inhibited nitrification in the first stage and therewith allowed the separation of organics depletion from nitrification. An organics removal of 70 % was achieved at organic loading rates in the influent of 3.7 gCOD d-1 m-2. Organics depletion in a continuous flow stirred tank reactor (CSTR) for organics depletion led to ammonia stripping through diffused aeration of up to 13 %. Using an MABR, diffusion into the lumen amounted for 4 % ammonia loss only. In the MABR, headspace volume and therefore ammonia loss through the headspace was negligible. By aerating the downstream MABR for nitrification with the off-gas of the MABR for organics depletion, 96 % of the ammonia stripped in the first stage could be recovered in the second stage, so that the overall ammonia loss was negligibly low. Nitrification of the organics-depleted urine was studied in MABRs, CSTRs, and sequencing batch reactors in fed batch mode (FBRs), the latter two operated with suspended biomass. The experiments demonstrated that upstream organics depletion can double the nitrification rate. In a laboratory-scale MABR, nitrification rates were recorded of up to 830 mgNL-1 d-1 (3.1 gN m-2 d-1) with ambient air and over 1500 mgNL-1 d-1 (6.7 gN m-2 d-1) with oxygen-enriched air. Experiments with a laboratory-scale MABR showed that increasing operational parameters such as pH, recirculation flow, scouring frequency, and oxygen content increased the nitrification rate. The nitrification in the MABR was robust even at high pH setpoints of 6.9 and was robust against process failures arising from operational mistakes. The hydraulic retention time (HRT) required for nitrification was only 1 to 2 days. With the preceding organics depletion, the HRT for our system requires 2 to 3 days in total, whereas a combined activated sludge system requires 4 to 8 days. The N2O concentration in the off-gas increases with increasing nitrification rates; however, the N2O emission factor was 2.8 % on average and independent of nitrification rates. These results indicate that the MABR technology has a high potential for efficient and robust production of ammonium nitrate from source-separated urine.

Dietary fiber alleviates alcoholic liver injury via Bacteroides acidifaciens and subsequent ammonia detoxification.

The gut microbiota and diet-induced changes in microbiome composition have been linked to various liver diseases, although the specific microbes and mechanisms remain understudied. Alcohol-related liver disease (ALD) is one such disease with limited therapeutic options due to its complex pathogenesis. We demonstrate that a diet rich in soluble dietary fiber increases the abundance of Bacteroides acidifaciens (B. acidifaciens) and alleviates alcohol-induced liver injury in mice. B. acidifaciens treatment alone ameliorates liver injury through a bile salt hydrolase that generates unconjugated bile acids to activate intestinal farnesoid X receptor (FXR) and its downstream target, fibroblast growth factor-15 (FGF15). FGF15 promotes hepatocyte expression of ornithine aminotransferase (OAT), which facilitates the metabolism of accumulated ornithine in the liver into glutamate, thereby providing sufficient glutamate for ammonia detoxification via the glutamine synthesis pathway. Collectively, these findings uncover a potential therapeutic strategy for ALD involving dietary fiber supplementation and B. acidifaciens.

Identification and functional analysis of circular RNA expression profiles associated with ammonia exposure in chicken lungs.

Ammonia acts as a detrimental atmospheric pollutant, posing a sever threat to respiratory tract health and causing lung injury in humans and animals. Circular RNAs (circRNAs) are a distinctive class of non-coding RNA generated by back-splicing of linear RNA, implicated in various biological processes. However, their role in the immune response of chicken lungs to ammonia exposure remains unclear. In this study, we examined the expression profiles of circRNAs in chicken lungs under ammonia stimulation. In total, 61 differentially expressed (DE) circRNAs were identified between the ammonia exposure and control groups, including 17 up-regulated and 44 down-regulated circRNAs. The source genes of these DE circRNAs were predominantly enriched in Influenza A, SNARE interactions in vesicular transport, and Notch signaling pathway. Notably, nine DE circRNAs (circNBAS, circMTIF2, circXPO1, circSNX24, circRAB11A, circARID3B, circUSP54, circPPARA, and circERG) were selected for validation the reliability and authenticity of RNA-seq data. Results showed the back-splicing circular structure, as well as the reliability and accuracy of RNA-seq data in quantifying circRNA expression, as the RT-qPCR results were in agreement with the RNA-seq data. Moreover, we constructed the circRNA-miRNA-mRNA regulatory networks and identified several regulatory networks in chicken lungs under ammonia stimulation, including circRAB11A-gga-miR-191b-3p-BRD2 and circARID3B-gga-miR-1696-CKS2. Taken together, our study delineates the circRNA expression profile and their potential roles in the immune response of chicken lungs to ammonia exposure. These findings offer insights into molecular mechanisms that may mitigate diseases associated with ammonia induced respiratory tract pollution in humans and animals.

Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China.

The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.

Dynamic pH regulation drives Nitrosomonas for high-rate stable acidic partial nitritation.

How to intensify the ammonia oxidation rate (AOR) is still a bottleneck impeding the technology development for the innovative acidic partial nitritation because the eosinophilic ammonia-oxidizing bacteria (AOB), such as Nitrosoglobus or Nitrosospira, were inhibited by the high-level free nitrous acid (FNA) accumulation in acidic environments. In this study, an innovative approach of dynamic acidic pH regulation control strategy was proposed to realize high-rate acidic partial nitritation driven by common AOB genus Nitrosomonas. The acidic partial nitrification process was carried out in a laboratory-scale sequencing batch moving bed biofilm reactor (SBMBBR) for long-term (700 days) to track the effect of dynamic acidic pH on nitrifying bacterial activity. The results indicated that the influent NH4+-N concentration was about 100 mg/L, the nitrite accumulation ratio was exceeding 90%, and the maximum AOR can reach 14.5 ± 2.6 mg N L-1h-1. Although the half-saturation inhibition constant of NOB (KI_FNA(AOB)) reached 0.37 ± 0.10 mg HNO2N/L and showed extreme adaptability in FNA, the inactivation effect of FNA (6.1 mg HNO2N/L) for NOB was much greater than that of AOB, with inactivation rates of 0.61 ± 0.08 h-1 and 0.06 ± 0.01 h-1, respectively. The effluent pH was gradually reduced to 4.5 by ammonia oxidation process and the periodic FNA concentration reached 6.5 mg HNO2N/L to inactivate nitrite-oxidizing bacteria (NOB) without negatively affecting Nitrosomonas during long-term operation. This result provides new insights for the future implementation of high-rate stabilized acidic partial nitritation by Nitrosomonas.

[Start-up and Recovery Performance of ANAMMOX Reactors Under Long-term Starvation].

The application of ANAMMOX technology is constrained by sluggish growth and difficulty in enriching ANAMMOX bacteria. Long-term starvation of functioning bacteria due to limited substrate supply makes the steady operation of ANAMMOX reactors more difficult. Re-examining the start-up and recovery performance of the ANAMMOX reactor and identifying its resistance mechanism are important from the standpoint of long-term starvation. By inoculating nitrifying and denitrifying sludge under various operating circumstances, the ANAMMOX reactors were successfully started. Under various start-up procedures, the tolerance mechanism and recovery performance were examined. The outcomes demonstrated that the denitrifying sludge-inoculated reactor operated steadily with a high substrate concentration and low flow rate. After 85 days of operation, the removal efficiencies of NH4+-N, NO2--N, and total nitrogen reached 98.7%, 99.3%, and 89.3%, respectively. After 144 days of starvation and 30 days of recovery, the better nitrogen removal performance was achieved at a low substrate concentration and high flow rate, and the removal efficiencies were 99.8% （NH4+-N）, 99.8% （NO2--N）, and 93.6% （total nitrogen）. During the starvation, extracellular polymeric substances wrapped the ANAMMOX bacteria and kept them intact to resist long-term starvation stress. The expression of nirS, hzsA, and hdh genes ensured the synthesis of nitrite/nitric oxide oxidoreductase, hydrazine synthase, and hydrazine dehydrogenase to maintain ANAMMOX activity. There was no significant difference in the relative abundance of ANAMMOX bacteria before and after starvation recovery. Candidatus Kuenenia had better anti-hunger ability, and the relative abundance increased by more than 86% after 30 days of recovery, confirming its tolerance to long-term starvation.