Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification

Unraveling the effects and mechanisms of antibiotics on aerobic simultaneous nitrogen and phosphorus removal by Acinetobacter indicus CZH-5

The effects of antibiotics, such as tetracycline, sulfamethoxazole, and ciprofloxacin, on functional microorganisms are of significant concern in wastewater treatment. This study observed that Acinetobacter indicus CZH-5 has a limited capacity to remove nitrogen and phosphorus using antibiotics (5 mg/L) as the sole carbon source. When sodium acetate was supplied (carbon/nitrogen ratio = 7), the average removal efficiencies of ammonia-N, total nitrogen, and orthophosphate-P increased to 52.46 %, 51.95 %, and 92.43 %, respectively. The average removal efficiencies of antibiotics were 84.85 % for tetracycline, 39.32 % for sulfamethoxazole, 18.85 % for ciprofloxacin, and 23.24 % for their mixtures. Increasing the carbon/nitrogen ratio to 20 further improved the average removal efficiencies to 72.61 % for total nitrogen and 97.62 % for orthophosphate-P (5 mg/L antibiotics). Additionally, the growth rate and pollutant removal by CZH-5 were unaffected by the presence of 0.1-1 mg/L antibiotics. Transcriptomic analysis revealed that the promoted translation of aceE, aarA, and gltA genes provided ATP and proton -motive forces. The nitrogen metabolism and polyphosphate genes were also affected. The expression of acetate kinase, dehydrogenase, flavin mononucleotide enzymes, and cytochrome P450 contributed to antibiotic degradation. Intermediate metabolites were investigated to determine the reaction pathways.

Transcriptomic signature of bacteria exposed to benzalkonium chloride

The COVID-19 pandemic has highlighted our reliance on biocides, the increasing prevalence of resistance to biocides is a risk to public health. Bacterial exposure to the biocide, benzalkonium chloride (BAC), resulted in a unique transcriptomic profile, characterised by both a short and long-term response. Differential gene expression was observed in four main areas: motility, membrane composition, proteostasis, and the stress response. A metabolism shift to protect the proteome and the stress response were prioritised suggesting these are main resistance mechanisms. Whereas "well-established" mechanisms, such as biofilm formation, were not found to be differentially expressed after exposure to BAC.

Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments

BACKGROUND

Biological denitrification has been commonly adopted for the removal of nitrogen from sewage effluents. However, due to the low temperature during winter, microorganisms in the wastewater biological treatment unit usually encounter problems such as slow cell growth and low enzymatic efficiency. Hence, the isolation and screening of cold-tolerant aerobic denitrifying bacteria (ADB) have recently drawn attention. In our previous study, two Pseudomonas strains PMCC200344 and PMCC200367 isolated from Arctic soil demonstrated strong denitrification ability at low temperatures. The two Arctic strains show potential for biological nitrogen removal from sewage in cold environments. However, the genome sequences of these two organisms have not been reported thus far.

RESULTS

Here, the basic characteristics and genetic diversity of strains PMCC200344 and PMCC200367 were described, together with the complete genomes and comparative genomic results. The genome of Pseudomonas sp. PMCC200344 was composed of a circular chromosome of 6,478,166 bp with a G + C content of 58.60% and contained a total of 5,853 genes. The genome of Pseudomonas sp. PMCC200367 was composed of a circular chromosome of 6,360,061 bp with a G + C content of 58.68% and contained 5,801 genes. Not only prophages but also genomic islands were identified in the two Pseudomonas strains. No plasmids were observed. All genes of a complete set of denitrification pathways as well as various putative cold adaptation and heavy metal resistance genes in the genomes were identified and analyzed. These genes were usually detected on genomic islands in bacterial genomes.

CONCLUSIONS

These analytical results provide insights into the genomic basis of microbial denitrification in cold environments, indicating the potential of Arctic Pseudomonas strains in nitrogen removal from sewage effluents at low temperatures.

Genomics and nitrogen metabolic characteristics of a novel heterotrophic nitrifying-aerobic denitrifying bacterium Acinetobacter oleivorans AHP123

A novel aerobic strain of Acinetobacter oleivorans AHP123 was isolated from activated sludge, which could conduct heterotrophic nitrification and denitrification simultaneously. This strain has excellent NH₄⁺-N removal ability, with 97.93% removal rate at 24-hour. To identify the metabolic pathways of this novel strain, genes of gam, glnA, gdhA, gltB, nirB, nasA, nar, nor, glnK and amt were detected by genome analysis. Through RT-qPCR, it was found that the expression of key genes confirmed two possible ways of nitrogen removal in strain AHP123: nitrogen assimilation and heterotrophic nitrification aerobic denitrification (HNAD). However, the absence of some common HNAD genes (amo, nap and nos) suggested that strain AHP123 might have a different HNAD pathway from other HNAD bacteria. Nitrogen balance analysis revealed that strain AHP123 assimilated most of the external nitrogen sources into intracellular nitrogen.

Insight into the Cold Adaptation Mechanism of an Aerobic Denitrifying Bacterium: Bacillus simplex H-b

Psychrophilic bacteria with aerobic denitrification ability have promising potential for application in nitrogen-contaminated wastewater treatment, especially under cold conditions. A better understanding of the cold adaptation mechanism during aerobic denitrification would be beneficial for the practical application of this type of functional bacterium. In this study, Bacillus simplex H-b with good denitrification performance at 5°C was used to investigate the corresponding cold tolerance mechanism. Transcriptomics and nitrogen removal characterization experiments were conducted at different temperatures (5°C, 20°C, and 30°C). At low temperatures, more nitrogen was utilized for assimilation, accompanied by the accumulation of ATP and extracellular polymeric substances (EPS), rather than transforming inorganic nitrogen in the dissimilation pathway. In addition, the proportion of unsaturated fatty acids was higher in strains cultured at low temperatures. At the molecular level, the adjustment of membrane transport, synthesis of cofactors and vitamins, and transcriptional regulators might contribute to the survival of the strain under cold conditions. Moreover, nucleotide precursor synthesis, translation, and oxidative and temperature stress response mechanisms also enhanced the resistance of strain H-b to low temperatures. The results suggest that combining multiple regulatory mechanisms and synergistic adaptation to cold stress enabled the growth and relatively high nitrogen removal rate (27.22%) of strain H-b at 5°C. By clarifying the mechanism of regulation and cold resistance of strain H-b, a theoretical foundation for enhancing the application potential of this functional bacterium for nitrogen-contaminated wastewater treatment was provided. IMPORTANCE The newly isolated aerobic denitrifying bacterium Bacillus simplex H-b removed various forms of inorganic nitrogen (nitrate, nitrite, and ammonium) from wastewater, even when the temperature was as low as 5°C. Although this environmentally functional bacterium has been suggested as a promising candidate for nitrogen-contaminated water treatment at low temperatures, understanding its cold adaptation mechanism during aerobic denitrification is limited. In this study, the cold tolerance mechanism of this strain was comprehensively explained. Furthermore, a theoretical basis for the practical application of this type of functional bacterium for nitrogen removal in cold regions is provided. The study expands our understanding of the survival strategy of psychrophilic bacteria and hence supports their further utilization in wastewater treatment applications.

Aerobic denitrifying using actinobacterial consortium: Novel denitrifying microbe and its application

The aerobic denitrifying capacity of actinomycete strain has been investigated recently, while little is known about nitrogen and carbon substrate removal by mix-cultured aerobic denitrifying actinobacteria (Mix-CADA) community. Hence, three Mix-CADA consortiums, named Y23, X21, and Y27, were isolated from urban lakes to investigate their aerobic denitrification capacity, and their removal efficiency for nitrate and dissolved organic carbon were >97 % and 90 %, respectively. Illumina Miseq sequencing revealed that Streptomyces was the most dominant genus in the Mix-CADA consortium. Network analysis indicated that Streptomyces exfoliates, as the core species in the Mix-CADA consortium, majorly contributed to dissolved organic carbon and total nitrogen reduction. Moreover, the three Mix-CADA consortiums could remove 78 % of the total nitrogen and 61 % of the permanganate index from the micro-polluted l water. Meanwhile, humic-like was significantly utilized by three Mix-CADA consortiums, whereas Mix-CADA Y27 could also utilize aromatic protein and soluble microbial by-product-like in the micro-polluted raw water purification. In summary, this study will offer a novel perspective for the purification of micro-polluted raw water using the Mix-CADA consortium.

Insight into sulfamethoxazole effects on aerobic denitrification by strain Pseudomonas aeruginosa PCN-2: From simultaneous degradation performance to transcriptome analysis

It is a well-established fact that aerobic denitrifying strains are profoundly affected by antibiotics, but bacterium performing simultaneous aerobic denitrification and antibiotic degradation is hardly reported. Here, a typical aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 was discovered to be capable of sulfamethoxazole (SMX) degradation. The results showed that nitrate removal efficiency was decreased from 100% to 88.12%, but the resistance of strain PCN-2 to SMX stress was enhanced with the increment of SMX concentration from 0 to 100 mg/L. Transcriptome analysis revealed that the down-regulation of energy metabolism pathways rather than the denitrifying functional genes was responsible for the suppressed nitrogen removal, while the up-regulation of antibiotic resistance pathways (e.g., biofilm formation, multi-drug efflux system, and quorum sensing) ensured the survival of bacterium and the carrying out of aerobic denitrification. Intriguingly, strain PCN-2 could degrade SMX during aerobic denitrification. Seven metabolites were identified by the UHPLC-MS, and three degradation pathways (which includes a new pathway that has never been reported) was proposed combined with the expressions of drug metabolic genes (e.g., cytP450, FMN, ALDH and NAT). This work provides a mechanistic understanding of the metabolic adaption of strain PCN-2 under SMX stress, which provided a broader idea for the treatment of SMX-containing wastewater.

Different responses of representative denitrifying bacterial strains to gatifloxacin exposure in simulated groundwater denitrification environment

The impact of antibiotics on denitrification in the ecological environment has attracted widespread attention. However, the concentration threshold and inhibitory effect of the same antibiotic on denitrification mediated by mixed denitrifying microbes were conflicting in some studies. In this study, Paracoccus denitrificans, Acidovorax sp., and Pseudomonas aeruginosa were selected as representative denitrifying bacterial strains to explore the response of a single strain to gatifloxacin (GAT) exposure in groundwater denitrification. The results showed that the nitrate and nitrite removal efficiencies of Pseudomonas aeruginosa decreased by 34.87-36.25 % and 18.27-23.31 %, respectively, with exposure to 10 μg/L GAT, accompanied by a significant decline in denitrifying enzyme activity and gene expression. In contrast, the elevated denitrifying enzyme activity and gene expression of Paracoccus denitrificans promoted its nitrate and nitrite reduction by 2.09-10.00 % and 0-8.44 %, respectively. Additionally, there were no obvious effects on the removal of nitrate and nitrite by Acidovorax sp. in the presence of 10 μg/L GAT, which was consistent with the variation in denitrifying enzyme activity and total gene expression levels. The fit results of the Monod equation and its modification further elucidated the nitrate degradation characteristics from the perspective of denitrification kinetics. Furthermore, antibiotic resistance gene (ARG) analysis showed that the addition of 10 μg/L GAT (approximately 30 days) did not observably increase the relative abundance of ARGs. This study provides some preliminary understanding of the response differences of representative denitrifying bacterial strains to antibiotic exposure in groundwater denitrification.

A mechanistic review on aerobic denitrification for nitrogen removal in water treatment

The traditional biological nitrogen removal technology consists of two steps: nitrification by autotrophs in aerobic circumstances and denitrification by heterotrophs in anaerobic situations; however, this technology requires a huge area and stringent environmental conditions. Researchers reached the conclusion that the denitrification process could also be carried out in aerobic circumstances with the discovery of aerobic denitrification. The aerobic denitrification process is carried out by aerobic denitrifying bacteria (ADB), most of which are heterotrophic bacteria that can metabolize various forms of nitrogen compounds under aerobic conditions and directly convert ammonia nitrogen to N₂ for discharge from the system. Despite the fact that there is no universal agreement on the mechanism of aerobic denitrification, this article reviewed four current explanations for the denitrification mechanism of ADB, including the microenvironment theory, theory of enzyme, electron transport bottlenecks theory, and omics study, and summarized the parameters affecting the denitrification efficiency of ADB in terms of carbon source, temperature, dissolved oxygen (DO), and pH. It also discussed the current status of the application of aerobic denitrification in practical processes. Following the review, the difficulties of present aerobic denitrification technology are outlined and future research options are highlighted. This review may help to improve the design of current wastewater treatment facilities by utilizing ADB for effective nitrogen removal and provide the engineers with relevant references.

Microbial community and carbon-nitrogen metabolism pathways in integrated vertical flow constructed wetlands treating wastewater containing antibiotics

This study demonstrates effects of sulfamethoxazole (SMX) on carbon-nitrogen transformation pathways and microbial community and metabolic function response mechanisms in constructed wetlands. Findings showed co-metabolism of SMX with organic pollutants resulted in high removal of 98.92 ± 0.25% at influent concentrations of 103.08 ± 13.70 μg/L (SMX) and 601.92 ± 22.69 mg/L (COD), and 2 d hydraulic retention. Microbial community, co-occurrence networks, and metabolic pathways analyses showed SMX promoted enrichment of COD and SMX co-metabolizing bacteria like Mycobacterium, Chryseobacterium and Comamonas. Relative abundances of co-metabolic pathways like Amino acid, carbohydrate, and Xenobiotics biodegradation and metabolism were elevated. SMX also increased relative abundances of the resistant heterotrophic nitrification-aerobic denitrification bacteria Paracoccus and Comamonas and functional genes nxrA, narI, norC and nosZ involved in simultaneous heterotrophic nitrification-aerobic denitrification. Consequently, denitrification rate increased by 1.30 mg/(L∙d). However, insufficient reaction substrate and accumulation of 15.29 ± 2.30 mg/L NO₃^--N exacerbate inhibitory effects of SMX on expression of some denitrification genes.

Response of the aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 to low temperature and zinc oxide nanoparticles stress

Performance and molecular changes of an aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 have been investigated under different temperatures and ZnO nanoparticles (NPs) exposures. Strain HA-2 removed 95.7% of total nitrogen (TN) and 24.6% of phosphorus at 10 °C, which was attributed to the joint up-regulation of intracellular energy metabolism and ribosome. Moreover, with the increase of ZnO NPs from 0 to 100 mg/L, TN and phosphurs removal efficiencies decreased from 95.7% to 44.5% and 24.6% to 6.8% at 10 °C, respectively, whereas phosphorus removal rate increased from 10.5% to 24.5% at 20 °C. Further transcriptomics and proteomics revealed that significant down-regulation of purine and amino acid metabolisms was the main reason for the inhibitory effect at 10 °C, while the up-regulation of antioxidant pathways and functional genes expressions was responsible for the promoted phosphorus accumulation at 20 °C. This study provides a potential solution for improving biological nutrients removal processes in winter months.