The metabolic impact of extracellular nitrite on aerobic metabolism of Paracoccus denitrificans

Metabolomic reveals the responses of sludge properties and microbial communities to high nitrite stress in denitrifying phosphorus removal systems

Nitrite, as an electron acceptor, plays a good role in denitrifying phosphorus removal (DPR); however, high nitrite concentration has adverse affects on sludge performance. We investigated the precise mechanisms of responses of sludge to high nitrite stress, including surface characteristics, intracellular and extracellular components, microbial and metabolic responses. When the nitrite stress reached 90 mg/L, the sludge settling performance was improved, but the activated sludge was aging. FTIR and XPS analysis revealed a significant increase in the hydrophobicity of the sludge, resulting in improve settling performance. However, the intracellular carbon sources synthesis was inhibited. In addition, the components in the tightly bound extracellular polymeric substances (TB-EPS) of sludge were significantly reduced and indicated the disturb of metabolism. Notably, Exiguobacterium emerged as a new genus when face high nitrite stress that could maintaining survival in hostile environments. Moreover, metabolomic analysis demonstrated strong biological response to nitrite stress further supported above results that include the inhibited of carbohydrate and amino acid metabolism. More importantly, some lipids (PS, PA, LysoPA, LysoPC and LysoPE) were significantly upregulated that related enhanced membrane lipid remodeling. The comprehensive analyses provide novel insights into the high nitrite stress responses mechanisms in activated sludge systems.

Potential of free nitrous acid (FNA) for sludge treatment and resource recovery from waste activated sludge: A review

The escalating production of waste activated sludge (WAS) presents significant challenges to wastewater treatment plants (WWTPs). Free nitrous acid (FNA), known for its biocidal effect, has gained a growing focus on sludge dewatering, sludge reduction, and resource recovery from WAS due to its eco-friendly and cost-effective properties. Nevertheless, there have been no attempts made to systematically summarize or critically analyze the application of FNA in enhancing treatment and resource utilization of sludge. In this paper, we provided an overview of the current understanding regarding the application potential and influencing factors of FNA in sludge treatment, with a specific focus on enhancing sludge dewatering efficiency and reducing volume. To foster resource development from sludge, various techniques based on FNA have recently been proposed, which were comprehensively reviewed with the corresponding mechanisms meticulously discussed. The results showed that the chemical oxidation and interaction with microorganisms of FNA played the core role in improving resource utilization. Furthermore, current challenges and future prospects of the FNA-based applications were outlined. It is expected that this review can refine the theoretical framework of FNA-based processes, providing a theoretical foundation and technical guidance for the large-scale demonstration of FNA.

Isolation and characterization of novel 3,3'-iminodipropionitrile biodegrading Paracoccus communis, from an industrial wastewater treatment bioreactor

Until now, bacteria able to degrade, 3,3'-iminodipropionitrile (IDPN), a neurotoxin that destroys vestibular hair cells, causing ototoxicity, culminating in irreversible movement disorders, had never been isolated. The aim of this study was to isolate a novel IDPN-biodegrading microorganism and characterize its metabolic pathway. Enrichment was performed by inoculating activated sludge from a wastewater treatment bioreactor that treated IDPN-contaminated wastewater in M9 salt medium, with IDPN as the sole carbon source. A bacterial strain with a spherical morphology that could grow at high concentrations was isolated on a solid medium. Growth of the isolated strain followed the Monod kinetic model. Based on the 16S rRNA gene, the isolate was Paracoccus communis. Whole-genome sequencing revealed that the isolated P. communis possessed the expected full metabolic pathway for IDPN biodegradation. Transcriptome analyses confirmed the overexpression of the gene encoding hydantoinase/oxoprolinase during the exponential growth phase under IDPN-fed conditions, suggesting that the enzyme involved in cleaving the imine bond of IDPN may promote IDPN biodegradation. Additionally, the newly discovered P. communis isolate seems to metabolize IDPN through cleavage of the imine bond in IDPN via nitrilase, nitrile hydratase, and amidase reactions. Overall, this study lays the foundation for the application of IDPN-metabolizing bacteria in the remediation of IDPN-contaminated environments.

Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations

Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.

Discovery of a heterotrophic aerobic denitrification Pseudomonas sp. G16 and its unconventional nitrogen metabolic pathway

From the aerobic pond of the farm, the Pseudomonas sp. G16 was screened and isolated, which was confirmed to exhibit heterotrophic nitrification and aerobic denitrification. The removal rates of Ammonia (100 mg/L), nitrate (120 mg/L), and nitrite (100 mg/L) by the strain were 94.13%, 92.62%, and 85.67%, and the nitrogen metabolism pathway of strain G16 was analyzed by whole genome sequencing combined with its nitrification-denitrification intermediate products, it was found that the strain had independent nitrification-denitrification ability and no nitrite accumulation. Under the conditions of carbon source of sodium succinate hexahydrate, C/N ratio of 15, pH of 7.5, temperature of 15 °C, and DO of 210 rpm, strain G16 showed excellent denitrification performance. Strain G16 was prepared into biochar-based immobilized bacterial particles, which successfully improved its nitrogen removal efficiency and stability. Therefore, the application of strain G16 in the field of real wastewater treatment has very necessary research value.

Robustness and stability of acetate-driven partial denitrification (PD) in response to high COD/NO3--N

Partial Denitrification (PD) producing nitrite for anammox may face the issue of relatively high chemical oxygen demand (COD) loading (i.e., COD/NO₃^--N) due to real wastewater being changed in substrate concentration and flowrate. In this study, three PD systems (R1, R2, R3) with sodium acetate providing electrons were developed to investigate the influence of the relatively high COD/NO₃^--N ratios (4.0, 6.0, and 8.0) on NO₂^--N production and the subsequent recoverability. It was found that a relatively high NO₂^--N production with nitrate-to-nitrite transformation ratio (NTR) of 74.0% could be still obtained despite COD/NO₃^--N even improving to 8.0 under limited reaction time (10 min) with small nitrate remaining. However, a deteriorated nitrite production was observed with sufficient reaction time (15 min) with NTR being lowered to 19.2%. Delightedly, when reducing influent COD/NO₃^--N to a normal level of 3.0, PD with high nitrite production was rapidly achieved after suffering from a relatively high COD/NO₃^--N (4.0-8.0) for 130 cycles. Besides, it was found the relatively high COD/NO₃^--N had a minor influence on the recoverability of PD, as evidenced by the close NTRs. Microbial analysis revealed the relative abundance of PD functional bacteria, Thauera, decreased under high COD/NO₃^--N, while it is still highly dominated in the systems, varying from 75.1% in R1 to 62.8% in R3 after around 110-cycles recovery. Furthermore, it appeared that the high pH (9.1-9.2) induced by sodium acetate also likely played a role in maintaining the excellent PD. Overall, this study demonstrated the robustness and stability of acetate-driven PD in response to high COD/NO₃^--N, further informing the technological superiority of PD in supplying stable and efficient nitrite, which provided solid technical support to apply it with anammox for high-efficient N removal.

DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans

The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either dksA1 (one of two dksA homologs in the P. denitrificans genome) or relA/spoT (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in nap promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that nap promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The dksA1 and relA/spoT genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second dksA homolog (dksA2) and relA/spoT have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. IMPORTANCE Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.

Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture

The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.

Enhanced biological phosphorus and nitrogen removal by high-concentration powder carriers: extracellular polymeric substance, microbial communities, and metabolic pathways

In this study, diatomite, activated carbon, and iron-carbon (Fe-C) were used as biological carriers for the integrated fixed-film activated sludge process. Biomass, pollutant removal efficiency, and extracellular polymer were tested, and the effect of nitrogen and phosphorus removal, enzyme activity, and microbial diversity were studied after the sludge retention time was changed. The mechanism of carrier enriching microorganism and promoting pollutant degradation was studied. The results showed that the addition of these three carriers contributed to the enrichment of nitrifying bacteria in the system, and the NH₄⁺-N removal efficiency was above 98%. Diatomite and Fe-C could improve pollutant removal by increasing the activity of the electron transfer system. The abundance of denitrogenation-related reductases and the enzymes synthesizing poly-β-hydroxybutyrate was increased in activated carbon. The addition of Fe-C increased the abundance of denitrifying phosphate-accumulating organisms by approximately 25% and the removal efficiency of total phosphorus by 12.61-14.88% at the end of the long-term operation.

Preparation for Denitrification and Phenotypic Diversification at the Cusp of Anoxia: a Purpose for N2O Reductase Vis-à-Vis Multiple Roles of O2

Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O₂ repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the N₂O reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O₂ or N₂O. To test this, cells were exposed to gradual O₂ depletion or sudden anoxia and subsequent spikes of O₂ and N₂O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e^--acceptor deprivation and show that O₂ spiking leads to bet-hedging, while N₂O spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N₂O spike had much lower respiration rates than those rescued by the O₂ spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O₂. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy-limited systems. IMPORTANCE Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their N₂O emissions because all cells express NosZ, reducing N₂O to N₂, while a minority express NirS + Nor, reducing NO₂^- to N₂O. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O₂ or N₂O. We confirm such entrapment and the rescue of all cells by an N₂O spike but only a fraction by an O₂ spike. The results shed light on the role of O₂ repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic nirS expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of N₂O, which contribute to anthropogenic climate forcing.

Adaptive regulation of activated sludge's core functional flora based on granular internal spatial microenvironment

A great deal of efforts has been put into studying the influence of the external macroenvironment for activated sludge to survive on microbial community succession, while granular internal spatial microenvironment should be given equal attention, because it is more directly involved in the information exchange and material transfer among microorganisms. This study systematically investigated the effects of granular microenvironment on spatial colonization and composition of sludge's core functional flora, and the corresponding difference of biological treatment performance. High content of extracellular-proteins (67.53 mg/gVSS) or extracellular-polysaccharide (65.02 mg/gVSS) stimulated the microbial flocculation and aggregation of 0.5-1.5 mm granules (GS) or 1.5-3.0 mm granules (GM), respectively, which was resulted from excellent cell hydrophobicity (59.26%) or viscosity (3.47 mPa s), therefore, constituted relatively dense porous frame. More hollow space existed in 3.0-5.0 mm granules (GL), which formed loose skeleton with 0.213 mL/g of total pore volume and 17.21 nm of average pore size. Combining scanning electron microscope images and fluorescent in-situ hybridization based microbiological analysis, aerobic nitrifiers were observed to wrap or surround anaerobic bacteria, or facultative/anaerobic bacteria were self-encapsulated, which created granule's unique microenvironment with alternating aerobic and anaerobic zones. GS has the most rich organic matter degrading bacteria and anaerobic heterotrophic denitrifiers, while GM and GL presented the greatest relative abundance of facultative and aerobic denitrifiers, respectively. The activity of dehydrogenase and nitrogen invertase of GM showed be 1.32-3.09 times higher than those of GS and GL, contributing to its higher carbon and nitrogen removal. These findings highlight the importance of granular microenvironment to adaptive regulation of activated sludge's core functional flora and corresponding pollutant removal performance.

Application of aerobic denitrifier for simultaneous removal of nitrogen, zinc, and bisphenol A from wastewater

High concentrations of heavy metals and other pollutants affect microbial activity in the wastewater treatment system and impede biological denitrification process. In this study, a novel Zn(II)-resistant aerobic denitrifier (Pseudomonas stutzeri KY-37) was isolated with potential in Bisphenol A (BPA) biodegradation and removal. The capability of this denitrifier in removing nitrogen, zinc, and BPA was tested. Using 56 mg/L nitrate as the sole nitrogen source, its removal efficiency achieved 98.5% in 12 h. This novel denitrifier had a strong auto-aggregation (maximum 65.8%), a high hydrophobicity rate (maximum 88.2%), and a massive amount (maximum 41.1 mg/g cell dry weight) of extracellular polymeric substances (EPS) production. Moreover, Zn(II) removal efficiency reached more than 95% with the initial high concentrations of 200 mg/L. The maximum BPA removal efficiency reached 88.8% with initial 10 mg/L. The removal mechanism of BPA was further explored in terms of microbial degradation, EPS adsorption, and intermediate degradation products.

Coexistence of silver ion and tetracycline at environmentally relevant concentrations greatly enhanced antibiotic resistance gene development in activated sludge bioreactor

Antibiotic resistance has become a global public health problem. Recently, various environmental pollutants have been reported to induce the proliferation of antibiotic resistance. However, the impact of multiple pollutants (e.g., heavy metals and antibiotics), which more frequently occur in practical environments, is poorly understood. Herein, one widely distributed heavy metal (Ag⁺) and one frequently detected antibiotic (tetracycline) were chosen to investigate their coexisting effect on the proliferation of antibiotic resistance in the activated sludge system. Results show that the co-occurrence of Ag⁺ and tetracycline at environmentally relevant concentrations exhibited no distinct inhibition in reactor performances. However, they inhibited the respiratory activity by 42%, destroyed the membrane structure by 218%, and increased membrane permeability by 29% compared with the blank control bioreactor. Moreover, the relative abundances of target antibiotic resistance genes (ARGs) (e.g., tetA, bla_TEM-1, and sulII) in effluent after exposure of coexisting Ag⁺ and tetracycline were increased by 92-1983% compared with those in control reactor, which were 1.1-4.3 folds higher than the sum of the sole ones. These were possibly attributed to the enrichments of antibiotic-resistant bacteria. The results would illumine the coexisting effect of heavy metals and antibiotics on the dissemination of ARGs in activated sludge system.

Achieving synergetic treatment of sludge supernatant, waste activated sludge and secondary effluent for wastewater treatment plants (WWTPs) sustainable development

A novel process that combines partial nitrification, fermentation and Anammox-partial denitrification (NFAD) was proposed to co-treat ammonia rich sludge supernatant (NH₄⁺-N = 1194.1 mg/L), external WAS (MLSS = 22092.6 mg/L) and WWTP secondary effluent (NO₃^--N = 58.6 mg/L). Three separated reactors were used for partial nitrification (PN-SBR), integrated fermentation and denitrification (IFD-SBR) and combined Anammox-partial denitrification (AD-UASB), respectively. The process resulted in excellent nitrogen removal efficiency (NRE) of 98.7%, external sludge reduction efficiency (SRE) of 44.6% and external sludge reduction rate of 4.1 kg/m³ after 200 days of continuous operation. IFD-SBR and AD-UASB contributed towards 89.4% and 9.2% nitrogen removal, respectively. In AD-UASB, cooperation between Anammox bacteria (4.1% Candidatus Brocadia) and partial denitrifying bacteria (3.2% Thauera) resulted in significant stability of Anammox pathway, which contributed up to 84.1% nitrogen removal in the combined Anammox-partial denitrification process. NFAD saved up to 100% organic resource demand and 25% of aeration consumption compared with the traditional nitrification-denitrification process.

Mechanism of nitrite transporter NirC in motility, biofilm formation, and adhesion of avian pathogenic Escherichia coli

The Escherichia coli (E. coli) nirC gene encodes a nitrite transporter, which involved in transporting toxic nitrite (NO₂^-) from the environment into the bacteria. Although the deletion of nirC gene could cause changes in motility, adhesion in the previous study, and the virulence involved in the specified mechanism for pathogenic E. coli remains to be known. In the present work, we aimed to evaluate the role of NirC in a serotype O2:K1:H7 avian pathogenic Escherichia coli (APEC) strain. For this purpose, we generated a NirC-deficient mutant of APEC XM strain and examined its biological characteristics. The nirC gene deletion mutant enhanced ability of motility, decreased in biofilm formation, and it markedly reduced ability to adhere mouse brain microvascular endothelial cell b.End3 cells. For understanding its mechanism, sequentially we detected and found the stress regulator rpoS and its downstream genes csrA were up-regulated in NirC-deficient mutant while diguanylate cyclase gene dgcT was down-regulated. By high-performance liquid chromatography (HPLC) experiment, we demonstrated the concentration of intracellular 3',5'-cyclic diguanosine monophosphate (c-di-GMP) significantly decrease in nirC gene deletion mutant. Taken data together, we may make a conclusion with a possible signal pathway clue, due to NirC mutation, environmental NO₂^- accumulation leads to nitrite stress and inactivates c-di-GMP synthesis by stimulating the stress regulator RpoS, resulting in changes of biological characteristics.

Study of free nitrous acid (FNA)-based elimination of sulfamethoxazole: Kinetics, transformation pathways, and toxicity assessment

Free nitrous acid (FNA)-based applications have been broadly adopted in the development of novel wastewater management technologies, but a basic understanding of the effect of the chemical properties of FNA on the elimination of micropollutants is still lacking. This study aims to comprehensively evaluate FNA-based elimination of sulfamethoxazole (SMX), which is a typical species of sulphonamide antibiotics. Batch experiments were conducted under different influencing factors to investigate the antibiotics elimination processes. We found that FNA showed specific efficacy on sulphonamides characterized by sulfonamide and aniline functional groups, such as SMX. SMX degradation was affected by the initial SMX concentration, FNA concentration and solution pH and described by d[SMX]/dt=-0.29e^-1.69pH[SMX]^0.945[FNA]^1.35. The cationic forms of SMX were more reactive towards FNA-based active components. Sulfonamide bond (S-N or C-S bonds) cleavage, nitrosubstitution, deamination and radical oxidation were proposed to be the relevant transformation pathways. The FNA-based technique was not effective for diminishing toxicity, but this process could strongly control antibacterial activity.

Trace Metal Availability Affects Greenhouse Gas Emissions and Microbial Functional Group Abundance in Freshwater Wetland Sediments

We investigated the effects of trace metal additions on microbial nitrogen (N) and carbon (C) cycling using freshwater wetland sediment microcosms amended with micromolar concentrations of copper (Cu), molybdenum (Mo), iron (Fe), and all combinations thereof. In addition to monitoring inorganic N transformations (NO₃ ^-, NO₂ ^-, N₂O, NH₄ ⁺) and carbon mineralization (CO₂, CH₄), we tracked changes in functional gene abundance associated with denitrification (nirS, nirK, nosZ), dissimilatory nitrate reduction to ammonium (DNRA; nrfA), and methanogenesis (mcrA). With regards to N cycling, greater availability of Cu led to more complete denitrification (i.e., less N₂O accumulation) and a higher abundance of the nirK and nosZ genes, which encode for Cu-dependent reductases. In contrast, we found sparse biochemical evidence of DNRA activity and no consistent effect of the trace metal additions on nrfA gene abundance. With regards to C mineralization, CO₂ production was unaffected, but the amendments stimulated net CH₄ production and Mo additions led to increased mcrA gene abundance. These findings demonstrate that trace metal effects on sediment microbial physiology can impact community-level function. We observed direct and indirect effects on both N and C biogeochemistry that resulted in increased production of greenhouse gasses, which may have been mediated through the documented changes in microbial community composition and shifts in functional group abundance. Overall, this work supports a more nuanced consideration of metal effects on environmental microbial communities that recognizes the key role that metal limitation plays in microbial physiology.

The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase

Increasing atmospheric concentration of N₂O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N₂O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N₂O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N₂O. In addition, the biochemical properties of N₂O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N₂O reductase accessory genes. N₂O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N₂O reductase in an active state.

Performance and mechanism of carbon dioxide fixation by a newly isolated chemoautotrophic strain Paracoccus denitrificans PJ-1

CO₂ is regarded as a major contributor to the global warming. CO₂ utilization is promising to reduce the CO₂ emissions. Currently, the biofixation of CO₂ using chemoautotrophs has markedly gain interest in CO₂ utilization. In this study, a newly isolated chemoautotroph, Paracoccus denitrificans PJ-1, was used for the biofixation of CO₂ under anaerobic condition. Experimental results revealed that Paracoccus denitrificans PJ-1 achieved a high carbon fixation rate (13.25 mg·L^-1·h^-1) which was ∼10 times faster than the previous reported chemotrophic bacteria using thiosulfate as electron donor. The best CO₂ fixation activity of Paracoccus denitrificans PJ-1 was achieved at the pH value of 9.0 and CO₂ concentration of 20 vol%. Meanwhile, a high CO₂ fixation yield of 106.03 mg·L^-1 was reached. The presence of oxygen was adverse to the biofixation, indicating that strain PJ-1 was more suitable for CO₂ fixation in anaerobic environments. Carbon mass balance analysis revealed that the carbon from CO₂ was mainly fixed into the extracellular organic carbon rather than the biomass. GC-MS analysis and cbbL gene test revealed that Paracoccus denitrificans PJ-1 fixed CO₂ through the Calvin-Benson-Bassham cycle and mainly converted CO₂ to oxalic acid and succinic acid. Overall, the excellent CO₂ fixation capacity of Paracoccus denitrificans PJ-1 suggests that it had potential for CO₂ utilization.

Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate

Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.

Efficient nitrous oxide recovery from incineration leachate by a nosZ-deficient strain of Pseudomonas aeruginosa

In this study, nitrous oxide was recovered from a lab-scale moving-bed biofilm reactor (MBBR) treating partial nitrification-treated leachate supplemented with a nosZ-deficient strain of Pseudomonas aeruginosa. Batch culture tests with the nosZ-deficient strain determined that the threshold for free nitrous acid (FNA) inhibition was 0.016 mg/L and that FNA concentrations above this threshold severely inhibited denitrification and transcription of genes from the dissimilatory nitrate reduction pathway (narG, nirS, and norB). High nitrite removal and N₂O conversion efficiencies (>95%) were achieved with long-term operation of this MBBR. N₂O accounted for the majority of biogas (80%) produced when the MBBR was fed partial nitrification-treated leachate with high nitrite concentrations and the drainage ratio was adjusted to 30%. Bacterial community analysis revealed that the nosZ-deficient Pseudomonas strain remained metabolically active and was primarily responsible for denitrification processes in the reactor. This study presents a promising method for N₂O recovery from incineration leachate.

A comparative long-term operation using up-flow anaerobic sludge blanket (UASB) and anaerobic membrane bioreactor (AnMBR) for the upgrading of anaerobic treatment of N, N-dimethylformamide-containing wastewater

Synthetic industrial wastewater containing approximately 2000 mg/L N, N-dimethylformamide (DMF) was treated using a lab-scale anaerobic sludge blanket (UASB) and an anaerobic membrane bioreactor (AnMBR) in this study. The inoculum consisted of two sources of sludge: Co-culture of anaerobic digested sludge (ADS) with DMF-hydrolyzing activated sludge (DAS) for the AnMBR, and co-culture of anaerobic granular sludge (AGS) with DAS for the UASB. Effective DMF methanogenic degradation of nearly 100% removal was achieved in both reactors on the first day. Both reactors obtained excellent DMF removal efficiency and high methane production under a low organic loading rate (OLR) of around 3-4 g COD/L/d. However, excessive elevation of OLR significantly limited DMF hydrolysis. When OLR exceeded 6 g COD/L/d, the removal efficiency and methane production in both reactors dramatically dropped. Despite their different forms and shapes, the ADS and AGS both provide methanogens which are responsible for methanogenesis. The UASB tolerated a higher OLR while the AnMBR was limited by membrane fouling due to the increased sludge concentration. However, the AnMBR obtained high-quality effluent without suspended solid. Whether DMF can be effectively degraded depends on DAS, in which abundant DMF-hydrolyzing bacteria (DHB) provide sufficient quantities of the hydrolytic enzyme for effective hydrolysis of DMF. However, these DHB were facultative and were also identified as denitrifying bacteria which require nitrate as the electron acceptor or otherwise survive under the aerobic condition. They gradually decayed rather than proliferated and were outcompeted by methanogens. Therefore, it is conceivable that a slight dosage of nitrate would enrich the abundance of DHB in both the UASB and the AnMBR, and provide a sufficient quantity of enzymes for the DMF hydrolysis. The cultivation of the anaerobic DMF-degrading granular sludge using the UASB is considered an upgraded solution to the effective treatment of DMF-containing wastewater.

Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review

Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO₂⁻) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.

High-efficient nitrogen removal from mature landfill leachate and waste activated sludge (WAS) reduction via partial nitrification and integrated fermentation-denitritation process (PNIFD)

Biological nitrogen removal from mature landfill leachate is ineffective due to the extremely low carbon/nitrogen (C/N) ratio. Moreover, a large amount of waste activated sludge (WAS) is inevitably generated from WWTPs during the municipal sewage treatment process. In this study, an innovative process was developed to enhance nitrogen removal from low C/N (1:1) mature landfill leachate and to reduce the WAS during a 300-day operation. Two sequencing batch reactors (SBRs) were involved in this process. Firstly, the mature landfill leachate was pumped into an aerobic reactor to undergo partial nitrification (PN-SBR). Then, the PN-SBR effluent and WAS were pumped into an anoxic reactor to undergo integrated fermentation and denitritation (IFD-SBR). The pH profile was treated as a real-time parameter to precisely control the duration of the PN and IFD processes. Partial nitrification and integrated fermentation-denitritation (PNIFD) system achieved a total nitrogen removal efficiency of 95.0% and an average nitrogen removal rate (NRR) of 0.63 kg/m³·d during the last operational phase. Due to a variety of refractory contaminants, the effluent COD concentration was 1865.9 mg/L and a 19.7% COD removal efficiency was obtained under an influent concentration of 2324.5 mg/L. Compared with the traditional nitrogen removal process, PNIFD not only decreased requirements for oxygen by 25% and the external organic carbon by 100%, but also achieved simultaneous reduction of external WAS. More than 53.7% of the external sludge was reduced during the IFD-SBR operational cycle, with an average external sludge reduction rate (SRR) of 5.09 kg/m³·d. Fermentation/denitritation related microorganisms, such as Anaerolineaceae, Acidimicrobiaceae and Thauera, accounted for up to 41.5% of the total abundance in the IFD-SBR. Based on the long and stable operation, this study provides a simple and promising approach for synchronous nitrogen removal and WAS reduction.

A Central Small RNA Regulatory Circuit Controlling Bacterial Denitrification and N2O Emissions

N₂O is an important greenhouse gas and a major cause of ozone depletion. Denitrifying bacteria play vital roles in the production and consumption of N₂O in many environments. Complete denitrification consists of the conversion of a soluble N-oxyanion, nitrate (NO₃^-), to an inert gaseous N-oxide, dinitrogen (N₂). Incomplete denitrification can occur if conditions are prohibitive, for example, under conditions of low soil copper concentrations, leading to emission of N₂O rather than N₂. Although enzymatically well characterized, the genetic drivers that regulate denitrification in response to environmental and physiological cues are not fully understood. This study identified a new regulatory sRNA-based control mechanism for denitrification in the model denitrifying bacterium P. denitrificans. Overexpression of this sRNA slows the rate of denitrification. This report highlights that there are gaps in understanding the regulation of this important pathway which need to be filled if strategies for N₂O mitigation can be rationally and carefully developed.

Global atmospheric loading of the climate-active gas nitrous oxide (N₂O) continues to increase. A significant proportion of anthropogenic N₂O emissions arises from microbial transformation of nitrogen-based fertilizers during denitrification, making microbial N₂O emissions a key target for greenhouse gas reduction strategies. The genetic, physiological, and environmental regulation of microbially mediated N₂O flux is poorly understood and therefore represents a critical knowledge gap in the development of successful mitigation approaches. We have previously mapped the transcriptional landscape of the model soil-denitrifying bacterium Paracoccus denitrificans. Here, we show that a single bacterial small RNA (sRNA) can control the denitrification rate of P. denitrificans by stalling denitrification at nitrite reduction to limit production of downstream pathway intermediates and N₂O emissions. Overexpression of sRNA-29 downregulates nitrite reductase and limits NO and N₂O production by cells. RNA sequencing (RNA-seq) analysis revealed 53 genes that are controlled by sRNA-29, one of which is a previously uncharacterized GntR-type transcriptional regulator. Overexpression of this regulator phenocopies sRNA-29 overexpression and allows us to propose a model whereby sRNA-29 enhances levels of the regulator to repress denitrification under appropriate conditions. Our identification of a new regulatory pathway controlling the core denitrification pathway in bacteria highlights the current chasm in knowledge regarding genetic regulation of this pivotal biogeochemical process, which needs to be closed to support future biological and chemical N₂O mitigation strategies.

Enhancing the digestion of waste activated sludge through nitrite addition: insight on mechanism through profiles of extracellular polymeric substances (EPS) and microbial communities

Extracellular nitrite has been used to improve the digestion of waste activated sludge (WAS). However, the underlying mechanism remains largely unknown. In this study, WAS was treated with 0.2 gNO₂^--N/gVSS for 7 days and its performance was compared to that of aerobic and anaerobic treatments. The addition of nitrite had a distinct effect on the reduction of VSS/SS and the accumulation of soluble organics compared to the control reactors. As evident by the variations of extracellular polymeric substances (EPS), nitrite addition had a positive effect on decreasing protein. In particular, the decrease of protein mainly occurred in tightly bound EPS (TB-EPS), which caused sludge disintegration and enhanced sludge reduction. Additionally, the decrease of microbial diversity with nitrite addition was significant compared to the control reactors, accompany with a decrease of live/dead cells ratio and an increase of supernatant DNA concentration. This suggests that nitrite could cause cell death and lysis, resulting in sludge degradation. Thus, nitrite addition enhanced sludge treatment through the combined effect of TB-EPS disintegration and cell lysis. These findings will be useful for the optimization of sludge treatment process based on nitrite addition.

Anaerobic treatment of N,N-dimethylformamide-containing high-strength wastewater by submerged anaerobic membrane bioreactor with a co-cultured inoculum

The anaerobic treatment of wastewater containing approximately 2000 mg L^-1N,N-dimethylformamide (DMF) was conducted by a lab-scale submerged anaerobic membrane bioreactor (SAnMBR). The inoculum consisted of aerobic DMF-hydrolyzing activated sludge (DAS) and anaerobic digested sludge (ADS). A rapid start-up was achieved with thorough DMF methanogenic degradation on the first day. The results of a 250-day long-term experiment demonstrated that under a low organic loading rate (OLR) of 3.14-4.16 g COD L^-1 d^-1, SAnMBR maintained excellent DMF removal efficiency along with high methane conversion. However, the elevation of OLR significantly limited DMF hydrolysis. When OLR exceeded 6.54 g COD L^-1 d^-1, both removal efficiency and methane production dramatically dropped. The DMF-hydrolyzing bacteria originating from the DAS gradually decayed under the anaerobic condition, resulting in the weak hydrolysis of DMF. The shortening of hydraulic retention time (HRT) is not recommended for the SAnMBR because severe membrane fouling occurred when HRT was shortened to 8 h. To handle high OLRs, an appropriate solution is to maintain a low F/M ratio by increasing both the influent DMF concentration and sludge concentration. The high CH₄ content in the biogas, exceeding 85%, was shown to be the reason for the suitability of anaerobic treatment to DMF. Some improvements which would help to maintain the effective hydrolysis are proposed: a side-stream system to replenish DAS to the SAnMBR is helpful; slight dosage of nitrate could also help to enrich the DMF-hydrolyzing bacteria; and the co-digestion of DMF and other organics might be convenient to establish a stable DMF-degrading consortium.

Aerobic denitrification by Paracoccus sp. YF1 in the presence of Cu(II)

This study of Cu(II)'s impact on aerobic denitrification of Paracoccus sp. YF1 revealed that the denitrification rate decreased markedly from 99.8%, 98.0%, 68.7% to 16.3% when the concentrations of Cu(II) rose from 0, 0.01 mM, 0.05 mM to 0.1 mM, respectively. This outcome was confirmed by the successful test of OD₆₀₀, total protein and enzyme activities. As the concentration of Cu(II) increased from 0 to 0.1 mM, the total protein contents declined over a period of 48 h, and the activities of nitrate reductase (NR) and nitrite reductase (NIR) decreased remarkably during the first 24 h in a NO₃^- sufficient state. Meanwhile, the reduction of NO₃^- and NO₂^- was positively correlated with the expression level of NR and NIR. The removal rate of nitrate in the control treatment and different concentration of Cu(II) treatment fitted approximately to the zero-order model. Scanning electron microscopy (SEM) confirmed that the cell surfaces of Paracoccus sp. YF1 were disrupted when exposed to 0.1 mM Cu(II). The adsorption of Cu(II) onto the cells' surface was confirmed by Energy dispersive spectrometer (EDS), Fourier transform infrared spectra (FTIR), and X-ray photoelectron spectroscopy analysis (XPS). The insights obtained here regarding the influence of Cu(II) on aerobic denitrification will be of great significance for the treatment of heavy metals and nitrite co-existing sewage.

Insights into the methanogenic degradation of N, N-dimethylformamide: The functional microorganisms and their ecological relationships

The methanogenic degradation of N, N-dimethylformamide (DMF) was investigated using anaerobic digested sludge (ADS), aerobic activated sludge (AAS) and co-cultured sludge (CCS), respectively. Both the metabolic pathway and the corresponding microorganisms which function in the methanogenic degradation of DMF were elucidated. DMF was unable to be degraded anaerobically by ADS due to the lack of DMF-hydrolyzing bacteria. DMF can be effectively degraded by AAS, however, no methane was recovered under the aerobic condition. The co-culture of DMF-hydrolyzing bacteria and methanogens in the CCS allowed for both hydrolysis of DMF and methane production to proceed successfully under the anaerobic condition, realizing the complete conversion from DMF to methane. However, a niche overlap due to the competition for the intermediates lowered the abundance of DMF-hydrolyzing bacteria. The introduction of nitrate, timely replenishment of AAS, micro-aeration and co-digestion were likely to maintain a high abundance of DMF-hydrolyzing bacteria to ensure an effective hydrolysis.

Optimization of methane-dependent oxygenic denitrification in sequencing batch reactors by insights into the microbial interactions

Methane-dependent oxygenic denitrification (O2DN) is a promising technology used for reducing greenhouse gas emissions of nitrous oxide (N₂O) during wastewater treatment. Heterotrophic bacteria are associated with methane-dependent O2DN bacteria, and it has been proposed that metabolic cross-feeding occurs between the two populations above. In this study, a mathematical model was developed to describe the microbial processes and interactions between methane-dependent O2DN bacteria and associated heterotrophic bacteria in a sequencing batch reactor (SBR). A growth factor-dependent decoupling of metabolism and growth of methane-dependent O2DN bacteria was introduced into the model. Effects of influent substrates, operating parameters, and initial biomass on microbial community and reactor performance were then investigated, and the above parameters were optimized using the model. Results surprisingly show that organic matter in the influent greatly stimulated the growth of methane-dependent O2DN bacteria but slightly limited the increase of heterotrophic bacteria. This effect could be explained by the increased excretion of growth factors by heterotrophic bacteria and the intensified competition for nitrite when methane-dependent O2DN bacteria increased. These results will assist in providing a new understanding of microbial interactions in methane-dependent O2DN systems and offer a new and efficient strategy for operating methane-dependent O2DN reactors.

Inhibition by free nitrous acid (FNA) and the electron competition of nitrite in nitrous oxide (N2O) reduction during hydrogenotrophic denitrification

Hydrogenotrophic denitrification is a promising technology for nitrate removal from organic-deficient wastewater or groundwater, and the attention of nitrous oxide (N₂O) emission during this process is required. Both nitrite and free nitrous acid (FNA or HNO₂) were reported to exert significant effects on N₂O reduction in heterotrophic denitrification, whereas, little knowledge has been obtained in hydrogenotrophic denitrification. In this study, we conducted a series of batch tests to comprehensively investigate the effects of nitrite, pH and FNA on N₂O production and reduction in a hydrogenotrophic denitrification process. The results showed that N₂O reduction rate decreased under both conditions of low pH and presence of nitrite, which would exert synergetic inhibition on N₂O reduction. The potential mechanisms that give rise to the results included electron competition and FNA inhibition. Electron competition between nitrite and N₂O reductases occurred when both nitrite and N₂O were added, which might contribute to the decrease in the N₂O reduction rate. The electron supply, which was obtained from the uptake of molecular hydrogen, declined with increasing FNA concentration according to a logarithmic model (R² = 0.9240). Additionally, the electron consumption rate of N₂O reductase to nitrite reductase ratio was initially stable and then decreased with increasing FNA concentration. The inhibition of N₂O reduction by FNA was determined to be reversible. The study suggested that both of the electron supply and N₂O reduction in hydrogenotrophic denitrification could be inhibited by FNA.

Paracoccus versutus KS293 adaptation to aerobic and anaerobic denitrification: Insights from nitrogen removal, functional gene abundance, and proteomic profiling analysis

A novel strain KS293 exhibiting excellent aerobic and anaerobic denitrification performance was isolated and identified as Paracoccus versutus KS293. Nitrate nitrogen and total organic carbon could be effectively removed by P. versutus KS293 without nitrite accumulation, whilst 82% and 85% of total nitrogen was converted into gaseous products under aerobic and anaerobic conditions (P > .05), respectively. Based on the ratio of anaerobic to aerobic, relative abundance values were increased 1.41, 1.45, and 2.31 folds for nirS, nosZ, and narG, respectively. A comparison of the two-dimensional gel electrophoresis and principal component analysis showed significant differences in proteomic profiles between aerobic and anaerobic conditions. In total, 78 proteins that displayed fluctuations in relative expression were observed. 10 proteins including nitrate reductase, maintenance of cell membrane (TolA), and RNA polymerase-binding transcription factor (DksA) were differentially expressed. These findings demonstrated that P. versutus KS293 was effective for nitrogen removal under aerobic or anaerobic conditions.

Tuning the modular Paracoccus denitrificans respirome to adapt from aerobic respiration to anaerobic denitrification

Bacterial denitrification is a respiratory process that is a major source and sink of the potent greenhouse gas nitrous oxide. Many denitrifying bacteria can adjust to life in both oxic and anoxic environments through differential expression of their respiromes in response to environmental signals such as oxygen, nitrate and nitric oxide. We used steady-state oxic and anoxic chemostat cultures to demonstrate that the switch from aerobic to anaerobic metabolism is brought about by changes in the levels of expression of relatively few genes, but this is sufficient to adjust the configuration of the respirome to allow the organism to efficiently respire nitrate without the significant release of intermediates, such as nitrous oxide. The regulation of the denitrification respirome in strains deficient in the transcription factors FnrP, Nnr and NarR was explored and revealed that these have both inducer and repressor activities, possibly due to competitive binding at similar DNA binding sites. This may contribute to the fine tuning of expression of the denitrification respirome and so adds to the understanding of the regulation of nitrous oxide emission by denitrifying bacteria in response to different environmental signals.

Environmental and Genetic Determinants of Biofilm Formation in Paracoccus denitrificans

The bacterium Paracoccus denitrificans is a model for the process of denitrification, by which nitrate is reduced to dinitrogen during anaerobic growth. Denitrification is important for soil fertility and greenhouse gas emission and in waste and water treatment processes. The ability of bacteria to grow as a biofilm attached to a solid surface is important in many different contexts. In this paper, we report that attached growth of P. denitrificans is stimulated by nitric oxide, an intermediate in the denitrification pathway. We also show that calcium ions stimulate attached growth, and we identify a large calcium binding protein that is required for growth on a polystyrene surface. We identify components of a signaling pathway through which nitric oxide may regulate biofilm formation. Our results point to an intimate link between metabolic processes and the ability of P. denitrificans to grow attached to a surface.

The genome of the denitrifying bacterium Paracoccus denitrificans predicts the expression of a small heme-containing nitric oxide (NO) binding protein, H-NOX. The genome organization and prior work in other bacteria suggest that H-NOX interacts with a diguanylate cyclase that cyclizes GTP to make cyclic di-GMP (cdGMP). Since cdGMP frequently regulates attached growth as a biofilm, we first established conditions for biofilm development by P. denitrificans. We found that adhesion to a polystyrene surface is strongly stimulated by the addition of 10 mM Ca²⁺ to rich media. The genome encodes at least 11 repeats-in-toxin family proteins that are predicted to be secreted by the type I secretion system (TISS). We deleted the genes encoding the TISS and found that the mutant is almost completely deficient for attached growth. Adjacent to the TISS genes there is a potential open reading frame encoding a 2,211-residue protein with 891 Asp-Ala repeats. This protein is also predicted to bind calcium and to be a TISS substrate, and a mutant specifically lacking this protein is deficient in biofilm formation. By analysis of mutants and promoter reporter fusions, we show that biofilm formation is stimulated by NO generated endogenously by the respiratory reduction of nitrite. A mutant lacking both predicted diguanylate cyclases encoded in the genome overproduces biofilm, implying that cdGMP is a negative regulator of attached growth. Our data are consistent with a model in which there are H-NOX-dependent and -independent pathways by which NO stimulates biofilm formation.

IMPORTANCE The bacterium Paracoccus denitrificans is a model for the process of denitrification, by which nitrate is reduced to dinitrogen during anaerobic growth. Denitrification is important for soil fertility and greenhouse gas emission and in waste and water treatment processes. The ability of bacteria to grow as a biofilm attached to a solid surface is important in many different contexts. In this paper, we report that attached growth of P. denitrificans is stimulated by nitric oxide, an intermediate in the denitrification pathway. We also show that calcium ions stimulate attached growth, and we identify a large calcium binding protein that is required for growth on a polystyrene surface. We identify components of a signaling pathway through which nitric oxide may regulate biofilm formation. Our results point to an intimate link between metabolic processes and the ability of P. denitrificans to grow attached to a surface.