Modular DNA-Origami-Based Nanoarrays Enhance Cell Binding Affinity through the "Lock-and-Key" Interaction.

Surface proteins of cells are generally recognized through receptor-ligand interactions (RLIs) in disease diagnosis, but their nonuniform spatial distribution and higher-order structure lead to low binding affinity. Constructing nanotopologies that match the spatial distribution of membrane proteins to improve the binding affinity remains a challenge. Inspired by the multiantigen recognition of immune synapses, we developed modular DNA-origami-based nanoarrays with multivalent aptamers. By adjusting the valency and interspacing of the aptamers, we constructed specific nanotopology to match the spatial distribution of target protein clusters and avoid potential steric hindrance. We found that the nanoarrays significantly enhanced the binding affinity of target cells and synergistically recognized low-affinity antigen-specific cells. In addition, DNA nanoarrays used for the clinical detection of circulating tumor cells successfully verified their precise recognition ability and high-affinity RLIs. Such nanoarrays will further promote the potential application of DNA materials in clinical detection and even cell membrane engineering.

Multipathway of Nitrogen Metabolism Revealed by Genome-Centered Metatranscriptomics from Pyrite-Guided Mixotrophic Partial Denitrification/Anammox Installations.

Further reducing the organic requirements is essential for the sustainable development of partial denitrification/anammox technology. Here, an innovative mixotrophic partial denitrification/anammox (MPD/A) installation fed with pyrite and few organics was realized, and the average nitrogen and phosphorus removal rates were as high as 96.24 ± 0.11% and 79.23 ± 2.06%, respectively, with a C/N ratio of 0.5. To understand the nature by which MPD/A achieves efficient nitrogen removal and organic conservation, the electron transfer-dependent nitrogen escape and energy metabolism were first elucidated using multiomics analysis. Apart from heterotrophic denitrification and anammox, the results revealed some unexpected metabolic couplings of MPD/A systems, in particular, putative nitrate-dependent organic and pyrite oxidation among nominally heterotrophic Denitratisoma (PRO3) strains, which accelerated nitrate gasification with a low-carbon supply. Additionally, Candidatus Brocadia (AMX) employed extracellular solid-state electron acceptors as terminal electron sinks for high-rate ammonium removal. AMX transported ammonium electrons to extracellular γFeO(OH) (generated from pyrite oxidation) through the transient storage of menaquinoline pools, cytoplasmic migration via multiheme cytochrome(s), and OmpA protein/nanowires-mediated electron hopping on cell surfaces. Further investigation observed that extracellular electron flux resulted in the transfer of more energy from the increased oxidation of the electron donor to the ATP, supporting nitrite-independent ammonium removal.

Metagenomic insights into responses of microbial population and key functional genes to fulvic acid during partial nitritation.

The long-term impact of fulvic acid (FA) on partial nitritation (PN) system was initially examined in this study. The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate (NAR nearly 100%) and ammonium removal rate (ARR 56.85%), while FA over 50 mg/L decreased ARR from 56.85% to 0.7%. Sludge characteristics analysis found that appropriate FA (<50 mg/L) exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi. The analysis of metagenomics suggested that the presence of limited FA (0-50 mg/L) stimulated the generation of NADH, which favors the denitrification and nitrite reduction. The negative impact of FA on the PN system could be divided into two stages. Initially, limited FA (50-120 mg/L) was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria (Thauera). Increasing heterotrophs competed with AOB (Nitrosomonas) for dissolved oxygen, causing AOB to be eliminated and ARR to declined. Subsequently, when FA dosage was over 120 mg/L, Anaerolineae were inhibited and heterotrophic bacteria reduced, resulting in the abundance of AOB recovered. Nevertheless, the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced, leading to the deterioration of reactor performance. Overall, these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.

Multi-Omics Analysis Reveals the Nitrogen Removal Mechanism Induced by Electron Flow during the Start-up of the Anammox-Centered Process.

Significant progress in understanding the key enzymes or species of anammox has been made; however, the nitrogen removal mechanism in complex coupling systems centered on anammox remains limited. In this study, by the combination of metagenomics-metatranscriptomics analyses, the nitrogen removal in the anammox-centered coupling system that entails partial denitrification (PD) and hydrolytic acidification (HA, A-PDHA) was elucidated to be the nitrogen transformation driven by the electron generation-transport-consumption process. The results showed that a total nitrogen (TN) removal efficiency of >98%, with a TN effluence of <1 mg/L and a TN removal contribution via anammox of >98%, was achieved after 59 days under famine operation and alkaline conditions during the start-up process. Further investigation confirmed that famine operation promoted the activity of genes responsible for electron generation in anammox, and increased the abundance or expression of genes related to electron consumption. Alkaline conditions enhanced the electron generation for PD by upregulating the activity of glyceraldehyde 3-phosphate dehydrogenase and strengthened electron transfer by increasing the gene encoding quinone pool. Altogether, these variations in the electron flow led to efficient nitrogen removal. These results improve our understanding of the nitrogen removal mechanism and application of the anammox-centered coupling systems in treating nitrogen wastewater.

Sulfur-carbon loop enhanced efficient nitrogen removal mechanism from iron sulfide-mediated mixotrophic partial denitrification/anammox systems.

This study successfully established Iron Sulfide-Mediated mixotrophic Partial Denitrification/Anammox system, achieving nitrogen and phosphorus removal efficiency of 97.26% and 78.12%, respectively, with COD/NO3--N of 1.00. Isotopic experiments and X-ray Photoelectron Spectroscopy analysis confirmed that iron sulfide enhanced autotrophic Partial Denitrification performance. Meanwhile, various sulfur valence states functioned as electron buffers, reinforcing nitrogen and sulfur cycles. Microbial community analysis indicated reduced heterotrophic denitrifiers (OLB8, OLB13) under lower COD/NO3--N, creating more niche space for autotrophic bacteria and other heterotrophic denitrifiers. The prediction of functional genes illustrated that iron Sulfide upregulated genes related to carbon metabolism, denitrification, anammox and sulfur oxidation-reduction, facilitating the establishment of carbon-nitrogen-sulfur cycle. Furthermore, this cycle primarily produced electrons via nicotinamide adenine dinucleotide and sulfur oxidation-reduction processes, subsequently utilized within the electron transfer chain. In summary, the Partial Denitrification/Anammox system under the influence of iron sulfide achieved effient nitrogen removal by expediting electron transfer through the carbon-nitrogen-sulfur cycle.

Response of anammox consortia to inhibition from high ferroferric oxide nanoparticles concentration and potential recovery mechanism.

The substantial discharge of ferroferric oxide nanoparticles (Fe3O4 NPs) into sewage threatens the survival of functional microorganisms in wastewater treatment. This study elucidated responses of anaerobic ammonium oxidation (anammox) consortia to inhibition from high Fe3O4 NPs concentration and recovery mechanisms. The nitrogen removal efficiency decreased by 20.3 % and recovered after 55 days under 1000 mg/L Fe3O4 NPs concentration. Toxicity was attributed to reactive oxygen species (ROS) production. The excessive ROS damaged membrane integrity, nitrogen metabolism, and DNA synthesis, resulting in the inhibition of anammox bacteria activity. However, recovery mechanisms of anammox consortia activity were activated in response to 1000 mg/L Fe3O4 NPs. The increase of heme oxygenase-1, thioredoxin, and nicotinamide adenine dinucleotide-quinone oxidoreductase genes alleviated oxidative stress. Furthermore, the activation of metabolic processes associated with membrane and DNA repair promoted recovery of anammox bacteria activity. This study provided new insights into NPs contamination and control strategies during anammox process.

Efficient photocatalytic reduction of nitrate byproducts during anammox process by novel extracellular polymeric substances-embedded NH2-MIL-101(Fe) photocatalysts.

Anaerobic ammonium oxidation (anammox) is an efficient nitrogen removal process; however, nitrate byproducts hampered its development. In this study, extracellular polymeric substances (EPS) were embedded into NH2-MIL-101(Fe), creating NH2-MIL-101(Fe)@EPS to reduce nitrate. Results revealed that chemical nitrate reduction efficiency of NH2-MIL-101(Fe)@EPS surpassed that of NH2-MIL-101(Fe) by 17.3 %. After adding 0.5 g/L NH2-MIL-101(Fe)@EPS within the anammox process, nitrate removal efficiency reached63.9 %, consequently elevating the total nitrogen removal efficiency to 92.4 %. 16S rRNA sequencing results elucidated the predominant role of Candidatus Brocadia within NH2-MIL-101(Fe)@EPS-anammox system. Concurrently, sufficient photogenerated electrons were transferred to microorganisms, promoting the growth of Desnitratisoma and OLB17. Additionally, photogenerated electrons activated flavin and Complex III, thereby up-regulating crucial genes involved in intra/extracellular electron transfer. Subsequently, denitrification and dissimilatory nitrate reduction to ammonium were activated to reduce nitrate. In summary, this study achieved a notable rate of photocatalytic nitrate reduction within anammox process through the NH2-MIL-101(Fe)@EPS photocatalysts.

Impact mechanism and performance enhancement of ultrasound on ZVI-anammox system.

The zero-valent iron-anaerobic ammonium oxidation (ZVI-anammox) system has received widespread attention due to its excellent nitrogen removal performance and user-friendly operation. However, its disadvantages include a short service life, high ZVI consumption, and poor system stability. The use of ultrasound as a physical method is increasing in various water treatment processes. In this study, a series of batch tests were conducted to obtain the best ultrasonic parameter and explore the comprehensive effects of ultrasound on a ZVI-anammox system. The highest specific anammox activity of the ZVI-anammox system was found to be 2.88 mg total nitrogen/g of volatile suspended solids/h after ultrasonic treatment (0.2 w/mL, 5 min), which was 37.85% higher than a control group. Additionally, the service life of ZVI extended by 28.57% and the total nitrogen removal efficiency changed from 58.03-72.08 to 63.92-78.33% under ultrasonic irradiation. These phenomena were related to the mechanical force and cavitation of ultrasonic waves. Judging from the characteristics of sludge and ZVI, ultrasound can promote anammox sludge granulation, ease ZVI passivation, and enhance the stability of the entire system. This paper also briefly discusses the impact mechanisms of ultrasound on the ZVI-anammox system. In brief, ultrasound destroys the surface structure of ZVI and thus provides numerous attachment points for microorganisms that improve the performance of the entire system. The proposed ultrasound combined with ZVI is a novel method that has potential for use in large-scale engineering applications in actual sewage treatment after comprehensive analysis.

The molecular characteristics of dissolved organic matter in urbanized river sediments and their environmental impact under the action of microorganisms.

The complex relationships between the molecular composition of dissolved organic matter (DOM) and microbial communities are essential for maintaining the stability of aquatic ecosystems. This study comprehensively analyzed the characteristics and potential effects of DOM molecular composition as well as the relationship between microbial communities and DOM molecular composition in sediments from the Beiyun River, Beijing, China. The results showed that the content of DOM in Beiyun River sediments was 9.93-41.57 g/kg, mainly composed of lignin-like (36.75%) and protein-like (17.79%) substances. Compared with other rivers affected by anthropogenic activities, the higher content of labile substances in the Beiyun River increased the risk of nutrient release. At the same time, 1402 molecules remained stable in each sample, most of which were refractory lignin-like substances and protein-like substances carrying ester groups. The agricultural section contained more common DOM molecules than the urban section, mainly tannin-like and lignin-like substances with unsaturated or cyclic structures. And, the intensity of anthropogenic activities was the main reason affecting the diversity of unique DOM molecular in each sample. Moreover, Dechloromonas as the dominant genus of Proteobacteria was closely related to the biological modification of low unsaturated (DBE < 15) condensed aromatic compounds (P < 0.05). Anaerolineaceae and Anaerolineae belonging to the Chloroflexi phylum have the potential to degrade medium and high molecular weight (M/Z > 400) liable substances (P < 0.05) and release lignin-like substances. In addition, the proportion of protein-like substances can indirectly reflect the risk of nutrient release in sediments affected by urbanization. Thus, the results of this study further reveal the impact of urbanization on rivers, and provide theoretical basis and guidance for pollution control of the Beiyun River and other urbanized rivers worldwide.

Anammox-synchronous zero-valent iron oxidation promoting synergistic nitrogen and phosphorus removal from wastewater.

In this study, a novel process, anammox-synchronous zero-valent iron (ZVI) oxidationin whichnitrate byproductsare usedfor in situoxidization of ZVIwas first developed to simultaneously remove nitrogen and phosphorus from wastewater. The optimal ZVI dosage of 4 g/L significantly improved the nitrogen removal efficiency to 86.02 ± 1.98%, with the highest phosphorus removal efficiency enhanced from 39.62% to 98.97%. Several analytical techniques revealed that iron phosphate minerals formed by biologically induced mineralization promoted the phosphorus removal of the system and enhanced the settleability of granules. Candidatus Brocadia was the main anammox functional bacteria, which could promote the formation of iron phosphorus minerals. The increase of key functional genes involved in denitrification, especially narG, played a pivotal role in reducing nitrate to improve nitrogen removal performance. In addition, abundance regulation of gene fur enabled anammox bacteria always maintain high activity under different pH and ZVI dosages.

Metagenomics illuminated the mechanism of enhanced nitrogen removal and vivianite recovery induced by zero-valent iron in partial-denitrification/anammox process.

In this study, a novel strategy of zero-valent iron (ZVI) combined with acetic acid was proposed to optimize partial-denitrification/anammox (PD/A) process, and enhanced nitrogen removal mechanism was elucidated through metagenomics. Results showed that the optimal nitrogen and phosphorus removal were as high as 99.50% and 98.37%, respectively, with vivianite being precipitated as the main byproduct. The occurrence of Feammox was a crucial link for enhanced ammonia removal and vivianite recovery. Metagenomic analysis further certified that long-term acclimation of optimization strategy triggered DNRA-based nitrate reducing genes (narY/Z and nrfA) assigned to Candidatus Brocadia, which allow direct uptake of nitrate by the anammox. Additionally, ZVI might act as a new electron donor to decrease organics dependence of PD by reducing the abundance of genes for electron production involved in carbon metabolism. However, FA addition enhanced the relative abundances of genes involved in anammox including nitrogen reduction and oxidation, thereby accelerating nitrogen removal.

Rapid start-up strategy of partial denitrification and microbially driven mechanism of nitrite accumulation mediated by dissolved organic matter.

The rapid start-up of Partial denitrification (PD; nitrate to nitrite) was investigated based on the analysis of microbially driven mechanism of nitrite accumulation mediated by Dissolved organic matter (DOM) in this study. The nitrate to Nitrite transformation ratio (NTR) > 90% and effluent nitrate < 5 mg/L were achieved in 17 days by feeding with lower nitrate of ~ 35 mg/L and removing the idling period. And the enhanced nitrite accumulation when applying the above strategy is related to the decreased utilization of the aliphatic DOM during nitrite reduction process. Additionally, the rapid enriched Thauera and OLB13 (37.21%) and inhibited norank_f__Blastocatellaceae (2.86%), and the increased disparity (2.0-fold) between the genes involved in nitrite generation (e.g., narH) and for nitrite reduction (e.g., nirK) jointly contributed to PD start-up. While the genes (e.g., DLD) related to producing electrons from aliphatic DOM also up-regulated by 0.1-fold, which led to the increased nitrate removal and NTR.