Regulation of denitrification performance and microbial topology by lights: Insight into wavelength effects towards microbiota

Comprehensive revealing the destructive effect and inhibitory mechanism of oxytetracycline on aerobic denitrification bacteria Acinetobacter sp. AD1 based on cell state, electron behavior and intracellular environment

The wide application and low utilization rate of oxytetracycline (OTC) make it often detected in wastewater, which may cause harmful effects on microbial denitrification. Aerobic denitrification (AD) as a new microbial denitrification technology has obvious advantages. However, systematic studies on the effects of OTC on it are lacking. In this study, the effect of OTC on AD was comprehensively explored from multiple perspectives, the main results are as follows. From the perspective of bacterial performance, OTC inhibited AD bacteria growth, denitrification efficiency, and caused serious damage to cell morphological structure, results of CCK-8 confirmed that bacterial activity was significantly affected. From the perspective of electron behavior, OTC decreased electron-producing capacity of carbon metabolism, reduced activity of the electron transport system, inhibited the electron consumption of NAR and NIR to varying degrees, thus increased the risk of nitrite accumulation. From the perspective of intracellular environment, OTC broke redox balance and antioxidant mechanism, related carbon and nitrogen cycle functional genes were down-regulated, affected amino acid, organic acid and nucleotide metabolic processes. The above results provide important information for evaluating the potential risks of antibiotics on the application of AD, and provide key background and theoretical support for stabilizing the technology.

Promotion mechanisms of static magnetic field on sulfide-based partial autotrophic denitrification: Metabolic intermediates, electron behavior, oxidative stress, and microbial community

Sulfide-based Partial Autotrophic Denitrification (SPAD) coupled with anammox is a promising technology for simultaneous sulfide and nitrogen removal. Static magnetic field (SMF) has been recognized to facilitate biological denitrification processes, but the underlying mechanisms remain largely unexplored. In this study, the performance was investigated in long-term operation of SPAD process under SMF, aiming at exploring the potential of SMF to enhance the SPAD process. The results showed that the SMF reactor (R2) achieved 90.14 % nitrite accumulation, while it was 70.54 % in the control reactor (R1). SMF facilitated electron production, transfer and consumption, and increased the activity of Complex Ⅰ, Complex Ⅲ, Cyt.c, sulfide oxidase and nitrate reductase. In addition, SMF alleviated oxidative stress by reducing reactive oxygen species (ROS) production and promoting up-regulation of antioxidant defense systems. Real-time quantitative PCR and reverse transcription PCR combined with high-throughput sequencing analysis showed that SMF promoted the conversion of the dominant genus SOBII (Sulfurimonas) to SOBI (Thiobacillus), and the relative abundance of Thiobacillus in the R2 was 67.64 %, higher than that in the R1 (61.90 %). The study provides a new approach to achieve stable nitrite accumulation by the SPAD process as well as presents new insights into the role of SMF on microorganisms.

Polyphenolic compounds mitigate the oxidative damage of anammox sludge under long-term light irradiation

Continuous high-intensity light exposure can inhibit anaerobic ammonium oxidation (anammox) bacteria activity, though the specific impacts on anammox reactor performance remain unclear. This study investigates the effects of long-term light stress on anammox sludge reactors and explores the use of tea polyphenols as an engineering interventions to mitigate photo oxidation damage. The results showed that the nitrogen removal efficiency (NRE) of the reactor rapidly deteriorated to 41.4 % under 10,000 lx light conditions. However, reactors supplemented with 1 mg·L-1 and 5 mg·L-1 tea polyphenols sustained NREs of 75.2 % and 82.5 %, respectively. The addition of tea polyphenols alleviated oxidative stress by scavenging reactive oxygen species such as ·OH and H2O2, and by enhancing the activities of antioxidant enzymes including total superoxide dismutase and glutathione peroxidase. Candidatus Kuenenia was negatively impacted by light, while unclassified_f__Brocadiaceae thrived under light stress. These findings provide insights for the development of stable nitrogen removal systems under light exposure.

Metagenomics and metaproteomics reveal the effects of sludge types and inoculation modes on N,N-dimethylformamide degradation pathways and the microbial community involved

This study demonstrated the effects of the sludge type and inoculation method on the N,N-dimethylformamide degradation pathway and associated microbial communities. The sludge type is critical for DMF metabolism, with acclimatized aerobic sludge having a significant advantage in terms of DMF metabolism performance, whereas acclimatized anaerobic sludge has a reduced DMF metabolism capacity. Metagenomic revealed increased abundances of Methanosarcina, Pelomona and Xanthobacter in the adapted anaerobic sludge, suggesting that anaerobic sludge can utilize the methyl products produced by DMF metabolism for growth. Adapted aerobic sludge had high Mycobacterium abundance, significantly boosting DMF hydrolysis. In addition, a large number of dmfA2 genes were found in aerobic sludge, more so in acclimatized sludge, indicating stronger DMF metabolism. Conversely, acclimatized anaerobic sludge showed lower abundance of dmd-tmd and mauA/B, qhpA genes, implying long-term DMF toxicity reduced anaerobic microbial activity. Metaproteomic analysis showed that Methanosarcina and Methanomethylovorans enzymes in anaerobic sludge metabolized dimethylamine and methylamine to methane, aiding DMF degradation. In the aerobic sludge, aminohydrolase proteins, which hydrolyze DMF, were significantly upregulated. These findings provide insights into DMF wastewater treatment.

Intra/extracellular electron transfer and metagenomic analysis elucidated the roles of magnetic iron powder (Fe3O4) on mixotrophic denitrification system

Elemental iron provides a viable strategy to improve the denitrification efficiency by expediting electron transport. However, the roles of magnetic iron powder (Fe3O4) on mixotrophic denitrification remains unknown. In this study, the intra/extracellular electron transfer (IET/EET) and microbial metabolism mechanisms were explored in a Fe3O4-mediated sulfide-autotrophic and heterotrophic denitrification system. The results showed that Fe3O4 promoted the formation of dense clump structure with filamentous cross-linking in activated sludge. Fe3O4 could increase the coenzyme Q activity in IET and the content of free riboflavin and cytochrome c in EET. Metagenomic analysis indicated that denitrification, sulfide oxidation and sulfate reduction were the main pathways of nitrogen and sulfur metabolism, and the enriched denitrifying bacteria (Halomonas and Hypobacterium) and sulfur-oxidizing bacteria (Marinicella) could stably support nitrate removal. This study expands our understanding of the IET/EET during Fe3O4-mediated mixotrophic denitrification process, providing a novel insight for nitrogen removal from marine recirculating aquaculture wastewater.

Stable and antibacterial tannic acid-based covalent polymeric hydrogel for highly selective Pb2+ recovery from lead-acid battery industrial wastewater

The resource of trace lead (Pb2+) from wastewater bearing intricate components is imperative for sustainable progression of the lead-acid battery industry. Herein, we fabricated a tannic acid-based covalent polymeric hydrogel (TA@PMAM) with antimicrobial properties and stability via facile Michael addition reaction. The incorporation of tannic acid (TA) through robust covalent bond leads to a stable porous 3D covalent polymer network with almost no loss of mechanical properties even after 20 compression cycles. Batch adsorption experiments of TA@PMAM revealed an extraordinary adsorption capacity of Pb2+(Qe =196.6 mg/g), achieving 87.2 % of Pb2+ adsorption within the first 5 min owing to porous structure, numerous adsorption sites and good hydrophilicity. Moreover, TA@PMAM demonstrated a strong affinity for Pb2+ in the presence of the interfere metal ions (Cu2+, Co2+, Mn2+etc.) due to the carbonyl and phenolic hydroxyl that can specifically pair with Pb2+. Stable adsorption properties of TA@PMAM were confirmed in fixed bed column adsorption experiment using lead-acid batteries wastewater, retaining 79.56 % of initial adsorption capacity even after 10 times' reuse. Besides, TA@PMAM possesses a broad spectrum of antimicrobial properties. This study sheds novel light on the design and fabrication of adsorbent, which holds great potential for commercialization in recovering lead from battery industrial wastewater.

Mechanisms of anammox granular sludge reactor effluent as biostimulant: Shaping microenvironment for anammox metabolism

Effluent from anammox granular sludge (AnGS) bioreactor contains microbes and microbial products. This study explored mechanisms of utilizing AnGS-effluent as biostimulant for anammox process enhancement. Compared with no AnGS-effluent supplemented control reactor, 5.0 and 1.3 times higher ammonium nitrogen and total inorganic nitrogen removal rates, respectively were obtained with continuous AnGS-effluent supplementation after 98 days' operation. Anammox bacteria from Candidatus Brocadia accounted for 0.1 % (DNA level) and 1.3 %-1.5 % (RNA level) in control reactor, and 2.9 % (DNA level) and 54.5 %-55.4 % (RNA level) in the AnGS-effluent-fed reactor. Influent microbial immigration evaluation showed that bacterial immigration via AnGS-effluent supplementation was not the main contributor to active anammox community development. Amino acids biosynthesis, B-vitamins and coenzymes metabolism related pathways were facilitated by AnGS-effluent supplementation. AnGS-effluent supplementation aided anammox metabolic activity by shaping microenvironment and microbial interactions. This study provides insights into enhancing anammox bacterial metabolism with AnGS-effluent microbial products as biostimulant.

Multi-omics analysis of nitrifying sludge under carbon disulfide stress: Nitrification performance and molecular mechanisms

Carbon disulfide (CS2) is a widely used enzyme inhibitor with cytotoxic properties, commonly employed in viscose fibers and cellophane production due to its non-polar characteristics. In industry, CS2 is often removed by aeration, however, residual CS2 may enter the wastewater treatment plants, impacting the performance of nitrifying sludge. Currently, there is a notable dearth of research on the response of nitrifying sludge to CS2-induced stress. This study delves into the alterations in the performance of nitrifying sludge under short-term and long-term CS2 stress, scrutinizes the toxic effects of CS2 on microbial cells, elucidates the succession of microbial community structure, and delineates changes in microbial metabolic products. The findings from short-term CS2 stress revealed that low concentrations of CS2 induced oxidative stress damage, which was subsequently repaired in cells. However, at concentrations of 100-200 mg/L, CS2 inhibited reactive oxygen species, superoxide dismutase, and catalase, which are associated with metabolic and antioxidant activities. The inhibition of nitrite oxidoreductase activity by high concentrations of CS2 was attributed to its impact on the enzyme's conformation. Prolonged CS2 stress resulted in an increase in the secretion of soluble extracellular polymeric substances in sludge, while CS2 was assimilated into sulfate. The analysis of sludge microbial community structure revealed a decline in the relative abundance of Rhodanobacter, which is associated with nitrification, and an increase in Sinomonas, involved in sulfur oxidation. Metabolite analysis results demonstrated that high concentrations of CS2 affect pantothenate and CoA biosynthesis, purine metabolism, and glutathione metabolism. This study elucidated the microbial response mechanism of nitrifying sludge under short-term and long-term CS2 stress. It also clarified the composition and function of microbial ecosystems, and identified key bacterial species and metabolites. It provides a basis for future research to reduce CS2 inhibition through approaches such as the addition of metal ions, the selection of efficient CS2-degrading strains, and the modification of strain metabolic pathways.

Blue-light irradiation induced partial nitrification

The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.

Deciphering the potential role of quorum quenching in efficient aerobic denitrification driven by a synthetic microbial community

Low efficiency is one of the main challenges for the application of aerobic denitrification technology in wastewater treatment. To improve denitrification efficiency, a synthetic microbial community (SMC) composed of denitrifiers Acinetobacter baumannii N1 (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas hydrophila (AH) were constructed. The nitrate (NO3--N) reduction efficiency of the SMC reached 97 % with little nitrite (NO2--N) accumulation, compared to the single-culture systems and co-culture systems. In the SMC, AH proved to mainly contribute to NO3--N reduction with the assistance of AC, while PA exerted NO2--N reduction. AC and AH secreted N-hexanoyl-DL-homoserine lactone (C6-HSL) to promote the electron transfer from the quinone pool to nitrate reductase. The declined N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL), resulting from quorum quenching (QQ) by AH, stimulated the excretion of pyocyanin, which could improve the electron transfer from complex III to downstream denitrifying enzymes for NO2--N reduction. In addition, C6-HSL mainly secreted by PA led to the up-regulation of TCA cycle-related genes and provided sufficient energy (such as NADH and ATP) for aerobic denitrification. In conclusion, members of the SMC achieved efficient denitrification through the interactions between QQ, electron transfer, and energy metabolism induced by N-acyl-homoserine lactones (AHLs). This study provided a theoretical basis for the engineering application of synthetic microbiome to remove nitrate wastewater.

Rapid start-up sulfur-driven autotrophic denitrification granular process: Extracellular electron transfer pathways and microbial community evolution

Sulfur-driven autotrophic denitrification (SAD) granular process has significant advantages in treating low-carbon/nitrogen wastewater; however, the slow growth rate of sulfur-oxidizing bacteria (SOB) results in a prolonged start-up duration. In this study, the thiosulfate-driven autotrophic denitrification (TAD) was successfully initiated by inoculating anaerobic granular sludge on Day 7. Additionally, the electron donor was successfully transferred to the cheaper elemental sulfur from Day 32 to Day 54 at the nitrogen loading rate of 176.2 g N m-3 d-1. During long term experiment, the granules maintained compact structures with the α-helix/(β-sheet + random coil) of 29.5-40.1 %. Extracellular electron transfer (EET) pathway shifted from indirect to direct when electron donors were switched thiosulfate to elemental sulfur. Microbial analysis suggested that thiosulfate improved EET involving enzymes activity. Thiobacillus and Sulfurimonas were dominant in TAD, whereas Longilinea was enriched in elemental sulfur-driven autotrophic denitrification. Overall, this strategy achieved in-situ enrichment of SOB in granules, thereby shortening start-up process.

From mechanism to application: Decrypting light-regulated denitrifying microbiome through geometric deep learning

Regulation on denitrifying microbiomes is crucial for sustainable industrial biotechnology and ecological nitrogen cycling. The holistic genetic profiles of microbiomes can be provided by meta-omics. However, precise decryption and further applications of highly complex microbiomes and corresponding meta-omics data sets remain great challenges. Here, we combined optogenetics and geometric deep learning to form a discover-model-learn-advance (DMLA) cycle for denitrification microbiome encryption and regulation. Graph neural networks (GNNs) exhibited superior performance in integrating biological knowledge and identifying coexpression gene panels, which could be utilized to predict unknown phenotypes, elucidate molecular biology mechanisms, and advance biotechnologies. Through the DMLA cycle, we discovered the wavelength-divergent secretion system and nitrate-superoxide coregulation, realizing increasing extracellular protein production by 83.8% and facilitating nitrate removal with 99.9% enhancement. Our study showcased the potential of GNNs-empowered optogenetic approaches for regulating denitrification and accelerating the mechanistic discovery of microbiomes for in-depth research and versatile applications.

Removal of nitrate nitrogen by Pseudomonas JI-2 under strong alkaline conditions: Performance and mechanism

The nitrate nitrogen removal characteristics of Pseudomonas JI-2 under strong alkaline conditions and the composition and functional groups of extracellular polymeric substance were analyzed. Furthermore, nontargeted metabonomics and bioinformatics technology were used to investigate the alkaline tolerance mechanism. JI-2 removed 11.05 mg N/(L·h) of nitrate with the initial pH, carbon to nitrogen ratio and temperature were 11.0, 8 and 25 °C respectively. Even when the pH was maintained at 11.0, JI-2 could still effectively remove nitrate. JI-2 contains a large number of Na+/H+ antiporters, such as Mrp, Mnh (mnhACDEFG) and Pha (phaACDEFG), which can stabilize the intracellular acid-base environment, and SlpA can enable quick adaptation to alkaline conditions. Moreover, JI-2 responds to the strong alkaline environment by secreting more polysaccharides, acidic functional groups and compatible solutes and regulating key metabolic processes such as pantothenate and CoA biosynthesis and carbapenem biosynthesis. Therefore, JI-2 can survive in strong alkaline environments and remove nitrate efficiently.