Influence of the Pseudomonas quinolone signal on denitrification in Pseudomonas aeruginosa

Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates

Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.

Regulation of extracellular polymers based on quorum sensing in wastewater biological treatment from mechanisms to applications: A critical review

Extracellular polymeric substances (EPS) regulated by quorum sensing (QS) could directly mediate adhesion between microorganisms and form tight microbial aggregates. Besides, EPS have redox properties, which can facilitate electron transfer for promoting electroactive bacteria. Currently, the applications research on improving wastewater biological treatment performance based on QS regulated EPS have been widely reported, but reviews on the level of QS regulated EPS to enhance EPS function in microbial systems are still lacking. This work proposes the potential mechanisms of EPS synthesis by QS regulation from the viewpoint of material metabolism and energy metabolism, and summarizes the effects of QS on EPS synthesis. By synthesizing the role of QS in EPS regulation, we further point out the applications of QS-regulated EPS in wastewater biological treatment, which involve a series of aspects such as strengthening microbial colonization, mitigating membrane biofouling, improving the shock resistance of microbial metabolic systems, and strengthening the electron transfer capacity of microbial metabolic systems. According to this comprehensive review, future research on QS-regulated EPS should focus on the exploration of the micro-mechanisms, and economic regulation strategies for QS-regulated EPS should be developed, while the stability of QS-regulated EPS in long-term production experimental research should be further demonstrated.

Negative regulation of biofilm formation by nitric oxide sensing proteins

Biofilm-based infections pose a serious threat to public health. Biofilms are surface-attached communities of microorganisms, most commonly bacteria and yeast, residing in an extracellular polymeric substance (EPS). The EPS is composed of several secreted biomolecules that shield the microorganisms from harsh environmental stressors and promote antibiotic resistance. Due to the increasing prominence of multidrug-resistant microorganisms and a decreased development of bactericidal agents in clinical production, there is an increasing need to discover alternative targets and treatment regimens for biofilm-based infections. One promising strategy to combat antibiotic resistance in biofilm-forming bacteria is to trigger biofilm dispersal, which is a natural part of the bacterial biofilm life cycle. One signal for biofilm dispersal is the diatomic gas nitric oxide (NO). Low intracellular levels of NO have been well documented to rapidly disperse biofilm macrostructures and are sensed by a widely conserved NO-sensory protein, NosP, in many pathogenic bacteria. When bound to heme and ligated to NO, NosP inhibits the autophosphorylation of NosP's associated histidine kinase, NahK, reducing overall biofilm formation. This reduction in biofilm formation is regulated by the decrease in secondary metabolite bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). The NosP/NahK signaling pathway is also associated with other major regulatory systems in the maturation of bacterial biofilms, including virulence and quorum sensing. In this review, we will focus on recent discoveries investigating NosP, NahK and NO-mediated biofilm dispersal in pathogenic bacteria.

Pyochelin biotransformation by Staphylococcus aureus shapes bacterial competition with Pseudomonas aeruginosa in polymicrobial infections

Pseudomonas aeruginosa and Staphylococcus aureus are among the most frequently isolated bacterial species from polymicrobial infections of patients with cystic fibrosis and chronic wounds. We apply mass spectrometry guided interaction studies to determine how chemical interaction shapes the fitness and community structure during co-infection of these two pathogens. We demonstrate that S. aureus is equipped with an elegant mechanism to inactivate pyochelin via the yet uncharacterized methyltransferase Spm (staphylococcal pyochelin methyltransferase). Methylation of pyochelin abolishes the siderophore activity of pyochelin and significantly lowers pyochelin-mediated intracellular reactive oxygen species (ROS) production in S. aureus. In a murine wound co-infection model, an S. aureus mutant unable to methylate pyochelin shows significantly lower fitness compared with its parental strain. Thus, Spm-mediated pyochelin methylation is a mechanism to increase S. aureus survival during in vivo competition with P. aeruginosa.

Encephalartos natalensis, Their Nutrient-Cycling Microbes and Enzymes: A Story of Successful Trade-Offs

Encephalartos spp. establish symbioses with nitrogen (N)-fixing bacteria that contribute to soil nutrition and improve plant growth. Despite the Encephalartos mutualistic symbioses with N-fixing bacteria, the identity of other bacteria and their contribution to soil fertility and ecosystem functioning is not well understood. Due to Encephalartos spp. being threatened in the wild, this limited information presents a challenge in developing comprehensive conservation and management strategies for these cycad species. Therefore, this study identified the nutrient-cycling bacteria in Encephalartos natalensis coralloid roots, rhizosphere, and non-rhizosphere soils. Additionally, the soil characteristics and soil enzyme activities of the rhizosphere and non-rhizosphere soils were assayed. The coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis were collected from a population of >500 E. natalensis in a disturbed savanna woodland at Edendale in KwaZulu-Natal (South Africa) for nutrient analysis, bacterial identification, and enzyme activity assays. Nutrient-cycling bacteria such as Lysinibacillus xylanilyticus; Paraburkholderia sabiae, and Novosphingobium barchaimii were identified in the coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis. Phosphorus (P) cycling (alkaline and acid phosphatase) and N cycling (β-(D)-Glucosaminidase and nitrate reductase) enzyme activities showed a positive correlation with soil extractable P and total N concentrations in the rhizosphere and non-rhizosphere soils of E. natalensis. The positive correlation between soil enzymes and soil nutrients demonstrates that the identified nutrient-cycling bacteria in E. natalensis coralloid roots, rhizosphere, and non-rhizosphere soils and associated enzymes assayed may contribute to soil nutrient bioavailability of E. natalensis plants growing in acidic and nutrient-poor savanna woodland ecosystems.

Molecular Mechanisms and Applications of N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Bacteria

Microbial biodiversity includes biotic and abiotic components that support all life forms by adapting to environmental conditions. Climate change, pollution, human activity, and natural calamities affect microbial biodiversity. Microbes have diverse growth conditions, physiology, and metabolism. Bacteria use signaling systems such as quorum sensing (QS) to regulate cellular interactions via small chemical signaling molecules which also help with adaptation under undesirable survival conditions. Proteobacteria use acyl-homoserine lactone (AHL) molecules as autoinducers to sense population density and modulate gene expression. The LuxI-type enzymes synthesize AHL molecules, while the LuxR-type proteins (AHL transcriptional regulators) bind to AHLs to regulate QS-dependent gene expression. Diverse AHLs have been identified, and the diversity extends to AHL synthases and AHL receptors. This review comprehensively explains the molecular diversity of AHL signaling components of Pseudomonas aeruginosa, Chromobacterium violaceum, Agrobacterium tumefaciens, and Escherichia coli. The regulatory mechanism of AHL signaling is also highlighted in this review, which adds to the current understanding of AHL signaling in Gram-negative bacteria. We summarize molecular diversity among well-studied QS systems and recent advances in the role of QS proteins in bacterial cellular signaling pathways. This review describes AHL-dependent QS details in bacteria that can be employed to understand their features, improve environmental adaptation, and develop broad biomolecule-based biotechnological applications.

Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.

Exploring the Function of Quorum Sensing Regulated Biofilms in Biological Wastewater Treatment: A Review

Quorum sensing (QS), a type of bacterial cell–cell communication, produces autoinducers which help in biofilm formation in response to cell population density. In this review, biofilm formation, the role of QS in biofilm formation and development with reference to biological wastewater treatment are discussed. Autoinducers, for example, acyl-homoserine lactones (AHLs), auto-inducing oligo-peptides (AIPs) and autoinducer 2, present in both Gram-negative and Gram-positive bacteria, with their mechanism, are also explained. Over the years, wastewater treatment (WWT) by QS-regulated biofilms and their optimization for WWT have gained much attention. This article gives a comprehensive review of QS regulation methods, QS enrichment methods and QS inhibition methods in biological waste treatment systems. Typical QS enrichment methods comprise adding QS molecules, adding QS accelerants and cultivating QS bacteria, while typical QS inhibition methods consist of additions of quorum quenching (QQ) bacteria, QS-degrading enzymes, QS-degrading oxidants, and QS inhibitors. Potential applications of QS regulated biofilms for WWT have also been summarized. At last, the knowledge gaps present in current researches are analyzed, and future study requirements are proposed.

Sorption of N-acyl homoserine lactones on maize straw derived biochars: Characterization, kinetics and isotherm analysis

Soil amendment with biochar may trigger a series of positive and negative biological effects, partly because it interferes quorum sensing (QS) signals synthesized by microorganisms for communication. However, the mechanisms through which biochar interacts with these QS signals remain elusive. This study explored the mechanisms of interactions between N-acyl homoserine lactones (AHLs) and two maize straw-derived biochars (MBs) with different pyrolysis temperature. Pseudo-second-order equation model best depicted AHLs sorption kinetics on MBs. The intra-particle diffusion model revealed that AHLs sorption onto MBs consists of several stages. The sorption isotherms data of AHLs on MBs were in well agreement with both Langmuir and Freundlich models, indicating the occurrence of energetic distribution of active sites on the heterogeneous biochar with multilayer sorption. However, the AHLs sorption capacity on MBs varied, with biochar pyrolyzed at 600 °C displaying a higher AHLs sorption capacity compared with biochar pyrolyzed at 300 °C. It may be attributed to a variety of physiochemical interactions such as pore filling, functional groups complexation, hydrogen bond, and hydrophobic action. The adsorption/partitioning model results and thermodynamic parameters of Gibbs free energy (ΔG) confirmed that physical and chemical sorption occurred concurrently throughout the whole AHLs sorption process, with physical partitioning playing a greater role than surface sorption. The findings suggest that soil amendment with biochar may have a variety of effects on intra/inter-cellular communication, further implying biochar can be specially prepared to mediate soil processes related to microbial communication, like pollutant biodegradation, and carbon/nitrogen cycling.

A Commensal Streptococcus Dysregulates the Pseudomonas aeruginosa Nitrosative Stress Response

Chronic infections in the cystic fibrosis (CF) airway are composed of both pathogenic and commensal bacteria. However, chronic Pseudomonas aeruginosa infections are the leading cause of lung deterioration in individuals with CF. Interestingly, oral commensals can translocate to the CF lung and their presence is associated with improved lung function, presumably due to their ability to antagonize P. aeruginosa. We have previously shown that one commensal, Streptococcus parasanguinis, produces hydrogen peroxide that reacts with nitrite to generate reactive nitrogen intermediates (RNI) which inhibit P. aeruginosa growth. In this study, we sought to understand the global impact of commensal-mediated RNI on the P. aeruginosa transcriptome. RNA sequencing analysis revealed that S. parasanguinis and nitrite-mediated RNI dysregulated expression of denitrification genes in a CF isolate of P. aeruginosa compared to when this isolate was only exposed to S. parasanguinis. Further, loss of a nitric oxide reductase subunit (norB) rendered an acute P. aeruginosa isolate more susceptible to S. parasanguinis-mediated RNI. Additionally, S. parasanguinis-mediated RNI inactivated P. aeruginosa aconitase activity. Lastly, we report that P. aeruginosa isolates recovered from CF individuals are uniquely hypersensitive to S. parasanguinis-mediated RNI compared to acute infection or environmental P. aeruginosa isolates. These findings illustrate that S. parasanguinis hinders the ability of P. aeruginosa to respond to RNI, which potentially prevents P. aeruginosa CF isolates from resisting commensal and host-induced RNI in the CF airway.

A Single Shot of Vesicles

Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling molecules by several bacteria. However, limited information is currently available on the mechanisms by which these molecules are transported between cells. Membrane vesicles (MVs) with diverse functions play important roles in the release and delivery of hydrophobic signaling molecules, leading to differences in the dynamics of signal transportation from those of free diffusion. Studies on Paracoccus denitrificans, which produces a hydrophobic long-chain N-acyl homoserine lactone (AHL), showed that signals were loaded into MVs at a concentration with the potential to trigger the quorum sensing (QS) response with a "single shot" to the cell. Furthermore, stimulating the formation of MVs increased the release of signals from the cell; therefore, a basic understanding of MV formation is important. Novel findings revealed the formation of MVs through different routes, resulting in the production of different types of MVs. Methods such as high-speed atomic force microscopy (AFM) phase imaging allow the physical properties of MVs to be analyzed at a nanometer resolution, revealing their heterogeneity. In this special minireview, we introduce the role of MVs in bacterial communication and highlight recent findings on MV formation and their physical heterogeneity by referring to our research. We hope that this minireview will provide basic information for understanding the functionality of MVs in ecological systems.

Quorum Sensing Regulation as a Target for Antimicrobial Therapy

Some bacterial species use a cell-to-cell communication mechanism called Quorum Sensing (QS). Bacteria release small diffusible molecules, usually termed signals which allow the activation of beneficial phenotypes that guarantee bacterial survival and the expression of a diversity of virulence genes in response to an increase in population density. The study of the molecular mechanisms that relate signal molecules with bacterial pathogenesis is an area of growing interest due to its use as a possible therapeutic alternative through the development of synthetic analogues of autoinducers as a strategy to regulate bacterial communication as well as the study of bacterial resistance phenomena, the study of these relationships is based on the structural diversity of natural or synthetic autoinducers and their ability to inhibit bacterial QS, which can be approached with a molecular perspective from the following topics: i) Molecular signals and their role in QS regulation; ii) Strategies in the modulation of Quorum Sensing; iii) Analysis of Bacterial QS circuit regulation strategies; iv) Structural evolution of natural and synthetic autoinducers as QS regulators. This mini-review allows a molecular view of the QS systems, showing a perspective on the importance of the molecular diversity of autoinducer analogs as a strategy for the design of new antimicrobial agents.

Effects of interactions between quorum sensing and quorum quenching on microbial aggregation characteristics in wastewater treatment: A review

Due to the increasingly urgent demand for effective wastewater denitrification and dephosphorization systems, there is a need to improve the performance of existing biological treatment technologies. As a bacteria-level communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. On this basis, the QS-based bacterial communication mechanism and environmental factors affecting QS are discussed. This paper reviews the influence of QS on sludge granulation, biofilm formation, emerging contaminants (ECs) removal, and horizontal gene transfer in sewage treatment system. Furthermore, the QS inhibition strategies are compared. Based on the coexistence and balance of QQ and QS in the long-term operation system, QQ, as an effective tool to regulate the growth density of microorganisms, provides a promising exogenous regulation strategy for residual sludge reduction and biofilm pollution control. This paper reviews the potential of improving wastewater treatment efficiency based on QS theory and points out the feasibility and prospect of exogenous regulation strategy. PRACTITIONER POINTS: The mechanism of bacterial communication based on QS and the environmental factors affecting QS were discussed. The application of QS and QQ in improving the sludge performance of biological treatment systems was described. The significance of QS and QQ coexistence in sewage treatment process was described.

Stigmasterol root exudation arising from Pseudomonas inoculation of the duckweed rhizosphere enhances nitrogen removal from polluted waters

Rhizospheric microorganisms such as denitrifying bacteria are able to affect 'rhizobioaugmention' in aquatic plants and can help boost wastewater purification by benefiting plant growth, but little is known about their effects on the production of plant root exudates, and how such exudates may affect microorganismal nitrogen removal. Here, we assess the effects of the rhizospheric Pseudomonas inoculant strain RWX31 on the root exudate profile of the duckweed Spirodela polyrrhiza, using gas chromatography/mass spectrometry. Compared to untreated plants, inoculation with RWX31 specifically induced the exudation of two sterols, stigmasterol and β-sitosterol. An authentic standard assay revealed that stigmasterol significantly promoted nitrogen removal and biofilm formation by the denitrifying bacterial strain RWX31, whereas β-sitosterol had no effect. Assays for denitrifying enzyme activity were conducted to show that stigmasterol stimulated nitrogen removal by targeting nitrite reductase in bacteria. Enhanced N removal from water by stigmasterol, and a synergistic stimulatory effect with RWX31, was observed in open duckweed cultivation systems. We suggest that this is linked to a modulation of community composition of nirS- and nirK-type denitrifying bacteria in the rhizosphere, with a higher abundance of Bosea, Rhizobium, and Brucella, and a lower abundance of Rubrivivax. Our findings provide important new insights into the interaction of duckweed with the rhizospheric bacterial strain RWX31 and their involvement in the aquatic N cycle and offer a new path toward more effective bio-formulations for the purification of N-polluted waters.

Impact of acyl-homoserine lactones on the response of nitrogen cycling in sediment to florfenicol stress

Antibiotic residuals disrupt environmental microbial metabolism and can alter the nitrogen cycle. Quorum sensing has both inter- and intra-species effects that are directly related to the population densities necessary for microbial nitrogen cycling. Here, we explored how acyl-homoserine lactones (AHLs) can change the response of nitrogen cycling to florfenicol in sediments. AHLs might promote microbial reproduction in sediment under florfenicol stress. The relative abundances of Proteobacteria and Euryarchaeota in the antibiotic and AHL treatment groups were higher than those in the control group. AHLs reduced the effects of antibiotics on the abundance of Nitrospira at sampling times of 3d, 10d, and 20d. In the annotation results, nitrate reductase showed the highest abundance, followed by nitrite reductase, nitrogenase, nitric oxide (NO) reductase, nitrous oxide reductase, and ammonia monooxygenase. The abundances of these genes have changed in response to pressure by florfenicol and the addition of AHLs. We also found significant associations between the nitrogen cycle-related functional genes and dominant genera. In particular, glutamate metabolic enzymes and nitrate/nitrite transporters were the primary participants in correlation. Florfenicol can rapidly alter microbial community structures in sediments, affect the functional diversity of microorganisms, and hinder the nitrogen cycle. The response of microorganisms to florfenicol was regulated by the addition of AHLs. This process might alter the use and production of nitrogenous substances in the environment by functional communities in sediments.

Biological and clinical significance of quorum sensing alkylquinolones: current analytical and bioanalytical methods for their quantification

Quorum sensing (QS) is a sophisticated bacterial communication system which plays a key role in the virulence and biofilm formation of many pathogens. The Pseudomonas aeruginosa QS network consists of four sets of connected systems (las, rlh, pqs and iqs) hierarchically organized. The pqs system involves characteristic autoinducers (AI), most of them sharing an alkylquinolone (AQ) structure, and is able to carry out several relevant biological functions besides its main signalling activity. Their role in bacterial physiology and pathogenicity has been widely studied. Indeed, the presence of these metabolites in several body fluids and infected tissues has pointed to their potential value as biomarkers of infection. In this review, we summarize the most recent findings about the biological implications and the clinical significance of the main P. aeruginosa AQs. These findings have encouraged the development of analytical and bioanalytical techniques addressed to assess the role of these metabolites in bacterial growth and survival, during pathogenesis or as biomarkers of infections. The availability of highly sensitive reliable analytical methods suitable for clinical analysis would allow getting knowledge about pathogenesis and disease prognosis or progression, supporting clinicians on the decision-making process for the management of these infections and guiding them on the application of more effective and appropriate treatments. The benefits from the implementation of the point-of-care (PoC)-type testing in infectious disease diagnostics, which are seen to improve patient outcomes by promoting earlier therapeutic interventions, are also discussed.

Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter

Understanding microbial interactions in the methanogenesis system through quorum sensing (QS) is very important for system optimization. Known QS genes were collected and classified into seven groups based on the signal molecules, which were used for constructing a hierarchical quorum sensing database (QSDB). QSDB containing 39,981 QS genes of seven QS groups was constructed and QS genes were analyzed with QSDB. Methanogen genomes were aligned with QSDB and acyl-homoserine lactones (AHLs) system was predicted as the most probable QS system. This database was further applied to analyze QS in methanogens from two upflow anaerobic sludge blanket-anaerobic filter hybrid reactors with conductive filter (CFB) and nonconductive filter (SEP), and a control without filter (CON). The maximum COD degradation rates in CFB (722.2 ± 10.1 mg/L·h) was elevated by 42.9% compared to CON (505.4 ± 5.98 mg/L·h). Metagenomic sequencing revealed Methanosaeta, Methanobacterium, and Methanosarcina were dominant, and the abundances was 4.3 times higher in the sludge of CFB compared to CON. The overall abundance of QS genes was CFB > SEP > CON, and AHLs were the most abundant group of QS genes. The filI/filR system, a luxI/luxR homolog, was firstly detected in methanogens, showing a high abundance in the CFB (0.085%) compared to in the CON (0.058%). The concentration of AHL molecules in CFB biofilms (0.04%) was about four times that in the CON (0.01%). Syntrophobacter and Smithella were the two major syntrophic bacteria of methanogens, and their abundances were positively correlated with methanogens. In addition, Syntrophobacter and Smithella harbored QS RpfB (component of the diffusible signal factor system) and PDE (component of cyclic di-GMP system). This study provides useful guidance for deeply understanding of QS in anaerobic digestion systems.

Function of quorum sensing and cell signaling in wastewater treatment systems

Quorum sensing (QS) is a communication mode between microorganisms to regulate bacteria ecological relations and physiological behaviors, thus achieve the physiological function that single bacteria cannot complete. This phenomenon plays important roles in the formation of biofilm and granular sludge, and may be related to enhancement of some functional bacteria activity in wastewater treatment systems. There is a need to better understand bacterial QS in engineered reactors, and to assess how designs and operations might improve the removal efficiency. This article reviewed the recent advances of QS in several environmental systems and mainly analyzed the regulation mechanism of QS-based strategies for biofilm, granular sludge, functional bacteria, and biofouling control. The co-existences of multiple signal molecules in wastewater treatment (WWT) processes were also summarized, which provide basis for the future research on the QS mechanism of multiple signal molecules' interaction in WWT. This review would present some prospects and suggestions which are of practical significance for further application.

Regulation of las and rhl Quorum Sensing on Aerobic Denitrification in Pseudomonas aeruginosa PAO1

The bacterium Pseudomonas aeruginosa negatively regulates denitrification under anerobic conditions by two acyl-homoserine lactone quorum-sensing (QS) systems called las and rhl. However, it is unknown whether these systems have the same effect on denitrification in aerobic conditions. In this study, we investigated the regulation of las and rhl systems on aerobic denitrification. We showed that the removal of nitrate in P. aeruginosa PAO1 was repressed by both the las and rhl systems. The las and rhl systems had negative effects on activities of denitrifying enzymes NAP, NIR, NOR, and NOS. At the level of transcription, both QS systems inhibited the expression of target genes napA, nirS, norB, norC, and nosZ. Furthermore, the addition of an acylase, which degrades the acyl-homoserine lactone signals (AHLs), to wild type resulted in an increase in the removal of nitrate. Additionally, in aerobic denitrification process, the transcription factor DNR, which controls denitrification, was repressed by both QS systems. The results implied that modulation of QS in denitrifying bacteria, possibly through quorum quenching or QS inhibition, could help to improve the reduction of nitrate in wastewater treatment.

Mapping of the Denitrification Pathway in Burkholderia thailandensis by Genome-Wide Mutant Profiling

Burkholderia thailandensis is a soil saprophyte that is closely related to the pathogen Burkholderia pseudomallei, the etiological agent of melioidosis in humans. The environmental niches and infection sites occupied by these bacteria are thought to contain only limited concentrations of oxygen, where they can generate energy via denitrification. However, knowledge of the underlying molecular basis of the denitrification pathway in these bacteria is scarce. In this study, we employed a transposon sequencing (Tn-Seq) approach to identify genes conferring a fitness benefit for anaerobic growth of B. thailandensis Of the 180 determinants identified, several genes were shown to be required for growth under denitrifying conditions: the nitrate reductase operon narIJHGK2K1, the aniA gene encoding a previously unknown nitrite reductase, and the petABC genes encoding a cytochrome bc ₁, as well as three novel regulators that control denitrification. Our Tn-Seq data allowed us to reconstruct the entire denitrification pathway of B. thailandensis and shed light on its regulation. Analyses of growth behaviors combined with measurements of denitrification metabolites of various mutants revealed that nitrate reduction provides sufficient energy for anaerobic growth, an important finding in light of the fact that some pathogenic Burkholderia species can use nitrate as a terminal electron acceptor but are unable to complete denitrification. Finally, we demonstrated that a nitrous oxide reductase mutant is not affected for anaerobic growth but is defective in biofilm formation and accumulates N₂O, which may play a role in the dispersal of B. thailandensis biofilms.IMPORTANCE Burkholderia thailandensis is a soil-dwelling saprophyte that is often used as surrogate of the closely related pathogen Burkholderia pseudomallei, the causative agent of melioidosis and a classified biowarfare agent. Both organisms are adapted to grow under oxygen-limited conditions in rice fields by generating energy through denitrification. Microoxic growth of B. pseudomallei is also considered essential for human infections. Here, we have used a Tn-Seq approach to identify the genes encoding the enzymes and regulators required for growth under denitrifying conditions. We show that a mutant that is defective in the conversion of N₂O to N₂, the last step in the denitrification process, is unaffected in microoxic growth but is severely impaired in biofilm formation, suggesting that N₂O may play a role in biofilm dispersal. Our study identified novel targets for the development of therapeutic agents to treat meliodiosis.

Synthesis and Antimicrobial Activity of Burkholderia-Related 4-Hydroxy-3-methyl-2-alkenylquinolines (HMAQs) and Their N-Oxide Counterparts

The Burkholderia genus offers a promising potential in medicine because of the diversity of biologically active natural products encoded in its genome. Some pathogenic Burkholderia spp. biosynthesize a specific class of antimicrobial 2-alkyl-4(1H)-quinolones, i.e., 4-hydroxy-3-methyl-2-alkenylquinolines (HMAQs) and their N-oxide derivatives (HMAQNOs). Herein, we report the synthesis of a series of six HMAQs and HMAQNOs featuring a trans-Δ² double bond at the C2-alkyl chain. The quinolone scaffold was obtained via the Conrad-Limpach approach, while the (E)-2-alkenyl chain was inserted through Suzuki-Miyaura cross-coupling under microwave radiation without noticeable isomerization according to the optimized conditions. Subsequent oxidation of enolate-protected HMAQs cleanly led to the formation of HMAQNOs following cleavage of the ethyl carbonate group. Synthetic HMAQs and HMAQNOs were evaluated in vitro for their antimicrobial activity against different Gram-negative and Gram-positive bacteria as well as against molds and yeasts. The biological results support and extend the potential of HMAQs and HMAQNOs as antimicrobials, especially against Gram-positive bacteria. We also confirm the involvement of HMAQs in the autoregulation of the Hmq system in Burkholderia ambifaria.

Technologies for biological removal and recovery of nitrogen from wastewater

Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.

The aerobic respiratory chain of Pseudomonas aeruginosa cultured in artificial urine media: Role of NQR and terminal oxidases

Pseudomonas aeruginosa is a Gram-negative γ-proteobacterium that forms part of the normal human microbiota and it is also an opportunistic pathogen, responsible for 30% of all nosocomial urinary tract infections. P. aeruginosa carries a highly branched respiratory chain that allows the colonization of many environments, such as the urinary tract, catheters and other medical devices. P. aeruginosa respiratory chain contains three different NADH dehydrogenases (complex I, NQR and NDH-2), whose physiologic roles have not been elucidated, and up to five terminal oxidases: three cytochrome c oxidases (COx), a cytochrome bo₃ oxidase (CYO) and a cyanide-insensitive cytochrome bd-like oxidase (CIO). In this work, we studied the composition of the respiratory chain of P. aeruginosa cells cultured in Luria Broth (LB) and modified artificial urine media (mAUM), to understand the metabolic adaptations of this microorganism to the growth in urine. Our results show that the COx oxidases play major roles in mAUM, while P. aeruginosa relies on CYO when growing in LB medium. Moreover, our data demonstrate that the proton-pumping NQR complex is the main NADH dehydrogenase in both LB and mAUM. This enzyme is resistant to HQNO, an inhibitory molecule produced by P. aeruginosa, and may provide an advantage against the natural antibacterial agents produced by this organism. This work offers a clear picture of the composition of this pathogen’s aerobic respiratory chain and the main roles that NQR and terminal oxidases play in urine, which is essential to understand its physiology and could be used to develop new antibiotics against this notorious multidrug-resistant microorganism.

Quorum sensing systems regulate heterotrophic nitrification-aerobic denitrification by changing the activity of nitrogen-cycling enzymes

Heterotrophic nitrification-aerobic denitrification (HNAD) is essential in diverse nitrogen-transforming processes. How HNAD is modulated by quorum sensing (QS) systems is still ambiguous. The QS system in Pseudomonas aeruginosa manipulates colony behavior. Here, we described the influence of the Pseudomonas quinolone signal (PQS) and N-acyl-l-homoserine lactone (AHL) on HNAD. The HNAD of P. aeruginosa was inhibited by the oversecretion of PQS. AHL- or PQS-deficient P. aeruginosa mutants had a higher ability for nitrogen removal. QS inhibited heterotrophic nitrification mainly via controlling the activity of nitrite oxidoreductase (NXR) and the depressed aerobic denitrification by regulating the catalytic abilities of nitric oxide reductase (NOR), nitrite reductase (NIR), and nitrate reductase (NAR). The addition of citrate as the sole carbon source increased the nitrogen removal efficiency compared with other carbon sources. Nitrite, as the sole nitrogen source, could be used entirely with only the moderate concentration of PQS contained. AHL and PQS controlled both nitrification and denitrification, suggesting that QS plays an important role in nitrogen cycle under aerobic conditions.

Transcriptome analysis reveals that the RNA polymerase-binding protein DksA1 has pleiotropic functions in Pseudomonas aeruginosa

The stringent response (SR) is a highly conserved stress response in bacteria. It is composed of two factors, (i) a nucleotide alarmone, guanosine tetra- and pentaphosphate ((p)ppGpp), and (ii) an RNA polymerase-binding protein, DksA, that regulates various phenotypes, including bacterial virulence. The clinically significant opportunistic bacterial pathogen Pseudomonas aeruginosa possesses two genes, dksA1 and dksA2, that encode DksA proteins. It remains elusive, however, which of these two genes plays a more important role in SR regulation. In this work, we compared genome-wide, RNA-Seq-based transcriptome profiles of ΔdksA1, ΔdksA2, and ΔdksA1ΔdksA2 mutants to globally assess the effects of these gene deletions on transcript levels coupled with phenotypic analyses. The ΔdksA1 mutant exhibited substantial defects in a wide range of phenotypes, including quorum sensing (QS), anaerobiosis, and motility, whereas the ΔdksA2 mutant exhibited no significant phenotypic changes, suggesting that the dksA2 gene may not have an essential function in P. aeruginosa under the conditions used here. Of note, the ΔdksA1 mutants displayed substantially increased transcription of genes involved in polyamine biosynthesis, and we also detected increased polyamine levels in these mutants. Because SAM is a shared precursor for the production of both QS autoinducers and polyamines, these findings suggest that DksA1 deficiency skews the flow of SAM toward polyamine production rather than to QS signaling. Together, our results indicate that DksA1, but not DksA2, controls many important phenotypes in P. aeruginosa We conclude that DksA1 may represent a potential target whose inhibition may help manage recalcitrant P. aeruginosa infections.

Mixture of different Pseudomonas aeruginosa SD-1 strains in the efficient bioaugmentation for synthetic livestock wastewater treatment

Strains selection for inoculation is the key to the successful construction of a bioaugmentation system, a promising strategy for specific pollutant removal. Pseudomonas aeruginosa SD-1 wild-type (WT) strain exhibited high capacity for biofilm formation but low efficiency for nitrate (NO₃^-) removal. Meanwhile, quorum sensing deficient strain ΔlasR showed excellent efficiency for NO₃^- removal but poor capability for colonization in activated sludge. The opposite effect of biofilm formation and NO₃^- removal exist in WT or ΔlasR, which limits the construction of bioaugmentation system of strain SD-1 and its application. To solve this issue, a mixture of WT and ΔlasR (v/v = 1:1) was used to construct a bioaugmentation system. Compared with the inoculation of WT or ΔlasR alone, the mixed inoculation not only was beneficial for activated sludge development but also for pollutant removal. The indicators for activated sludge including the abundance of P. aeruginosa, the sludge volume index and the average particle size in mixed inoculated reactors were close to those of reactors with single and repeated inoculation of WT. The effluent of chemical oxygen demand (COD) and NO₃^--N were stable at 3.9-22.6 mg L^-1 and 0-5.53 mg L^-1 after d 3, respectively. This study presents a detailed case on the ecological tradeoff of colonization and pollutant removal of inoculated strains during bioaugmentation. The results provide information on the appropriate conditions for application of P. aeruginosa SD-1 for livestock wastewater treatment and further enrich our ecological understanding of bioaugmentation.

Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms

The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.

Anaerobiosis influences virulence properties of Pseudomonas aeruginosa cystic fibrosis isolates and the interaction with Staphylococcus aureus

The airways of individuals with cystic fibrosis (CF) are abundantly colonised by Staphylococcus aureus and Pseudomonas aeruginosa. Co-infecting hypoxic regions of static mucus within CF airways, together with decreases in pulmonary function, mucus plugging and oxygen consumption by host neutrophils gives rise to regions of anoxia. This study determined the impact of anaerobiosis upon S. aureus-P. aeruginosa interactions in planktonic co-culture and mixed species biofilms in vitro. Whilst anoxia reduced the ability for P. aeruginosa CF isolates to dominate over S. aureus, this occurred in an isolate dependent manner. Investigations into the underlying mechanisms suggest that the anti-staphylococcal compound facilitating P. aeruginosa dominance under normoxia and anoxia is greater than 3 kDa in size and is heat-stable. Not all interspecies interactions studied were antagonistic, as S. aureus exoproducts were shown to restore and enhance P. aeruginosa motility under normoxia and anoxia in an isolate dependent manner. Collectively, this study suggests changes in oxygen availability within regions of the CF lung is likely to influence interspecies interactions and in turn, potentially influence disease progression.

Bacterial communication through membrane vesicles

Bacteria can communicate through diffusible signaling molecules that are perceived by cognate receptors. It is now well established that bacterial communication regulates hundreds of genes. Hydrophobic molecules which do not diffuse in aqueous environments alone have been identified in bacterial communication, that raised the question on how these molecules are transported between cells and trigger gene expressions. Recent studies show that these hydrophobic signaling molecules, including a long-chain N-acyl homoserine lactone signal produced in Paracoccus denitrificans, are carried by membrane vesicles (MVs). MVs were thought to be formed only through the blebbing of the cell membrane, but new findings in Pseudomonas aeruginosa and Bacillus subtilis revealed that different types of MVs can be formed through explosive cell lysis or bubbling cell death, which findings have certain implications on our view of bacterial interactions.

Roles of quorum sensing in biological wastewater treatment: A critical review

Quorum sensing (QS) and quorum quenching (QQ) are increasingly reported in biological wastewater treatment processes because of their inherent roles in biofilm development, bacterial aggregation, granulation, colonization, and biotransformation of pollutants. As such, the fundamentals and ubiquitous nature of QS bacteria are critical for fully understanding the process of the wastewater treatment system. In this article, the details of QS-based strategies related to community behaviors and phenotypes in wastewater treatment systems were reviewed. The molecular aspects and coexistence of QS and QQ bacteria were also mentioned, which provide evidence that future wastewater treatment will indispensably rely on QS-based strategies. In addition, recent attempts focusing on the use of QQ for biofilm or biofouling control were also summarized. Nevertheless, there are still several challenges and knowledge gaps that warrant future targeted research on the ecological niche, abundance, and community of QS- and QQ-bacteria in environmental settings or engineered systems.

Autotrophic nitrogen removal in combined nitritation and Anammox systems through intermittent aeration and possible microbial interactions by quorum sensing analysis

Nitrogen removal and microbial interactions in two combined nitritation and Anammox systems with or without the addition of organics were examined. Two systems were successfully started up by adopting intermittent aeration. Organics addition deteriorated nitrogen removal, and total inorganic nitrogen and ammonium removal percentages decreased by 16.4% and 26.3%, respectively. Organics addition promoted the growth of Chloroflexi and Proteobacteria while suppressed the growth of Candidatus Kuenenia. Organics addition decreased activities of fatty acid biosynthesis and metabolism, amino acid metabolism and biofilm formation, while increased activities of steroid metabolism and glycosaminoglycan biosynthesis. Heterotrophs and Candidatus Kuenenia might interact with other organisms by using diverse quorum sensing systems. Chloroflexi and Proteobacteria interacted with Candidatus Kuenenia in nitrogen metabolism and biofilm formation. Proteobacteria played a key role in building a nitrite loop with Candidatus Kuenenia and nitrifiers. These results clarified microbial interactions in the autotrophic nitrogen removal process and advance its application.

Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control

Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.

Dual-Edged Character of Quorum Sensing Signaling Molecules in Microbial Extracellular Electron Transfer

Quorum sensing (QS) is a central mechanism for regulating bacterial social networks in biofilm via the production of diffusible signal molecules (autoinducers). In this work, we assess the contribution of QS autoinducers to microbial extracellular electron transfer (EET) by Pseudomonas aeruginosa strain PAO1 and three mutants pure culture-inoculated in microbial electrolysis cells (MECs) and microbial fuel cells (MFCs). MECs inoculated with different P. aeruginosa strains showed a difference in current generation. All MFCs reached a reproducible cycle of current generation, and PQS-deficient pqsA mutant inoculated-MFCs obtained a much higher current generation than pqsL mutant inoculated-MFCs which overproduced PQS. lasIrhlI-inoculated MFCs produced a lower power output than others, as the strain was deficient in rhl and las. Exogenous N-butanoyl-l-homoserine lactone could remedy the electricity production by lasIrhlI mutants to a level similar to wild-type strains while signaling molecules had little effect on wild-type bacteria in MFCs. Meanwhile, experiments with the wild-type and pqsA, pqsL mutants indicated that the overexpression of PQS signaling molecules made no significant contribution to EET. QS signaling molecules therefore have dual-edged effects on microbial EET. These findings will provide favorable suggestions on the regulation of EET, but detailed QS regulatory mechanisms for extracellular electron transfer in pure- and mixed-cultures are yet to be elucidated.

Exogenous acyl-homoserine lactones adjust community structures of bacteria and methanogens to ameliorate the performance of anaerobic granular sludge

Quorum sensing (QS) signalling has been extensively studied in single species populations, activated sludge, biofilm and aerobic granular sludge. However, ecological roles of QS in anaerobic granular sludge, particularly in the content of the relationship between QS signalling and microbial community composition and function, have been rarely reported. Herein, five acyl-homoserine lactones (AHLs) molecules were added in the anaerobic granular sludge system for treating traditional Chinese medicine (TCM) wastewater respectively. The results indicated that the introduction of specific AHLs could enhance the abilities of organic matters removal and methanation in anaerobic granular sludge, and meanwhile, exogenous AHLs played an important role to regulate the concentration of EPS. Sequencing analysis indicated that microbial community structures of bacteria and methanogens changed to varying degrees by adding AHLs. This study suggested that exogenous AHLs could play a role in mediating microbial community structure, thereby enhancing the performance of anaerobic granular sludge. The regulatory mechanism of AHLs on community structure was discussed, and a speculative action model was established. Exogenous regulation by selective enhancement of AHLs-mediated QS in anaerobic granular sludge provided an innovative and attractive strategy for strengthening wastewater treatments.

The Pseudomonas Quinolone Signal (PQS): Not Just for Quorum Sensing Anymore

The Pseudomonas quinolone signal (PQS) has been studied primarily in the context of its role as a quorum-sensing signaling molecule. Recent data suggest, however, that this molecule may also function to mediate iron acquisition, cytotoxicity, outer-membrane vesicle biogenesis, or to exert host immune modulatory activities.

Reciprocal cross-species induction of outer membrane vesicle biogenesis via secreted factors

Delivery of cargo to target cells is fundamental to bacterial competitiveness. One important but poorly understood system, ubiquitous among Gram-negative organisms, involves packaging cargo into outer membrane vesicles (OMVs). These biological nanoparticles are involved in processes ranging from toxin delivery to cell-cell communication. Despite this, we know comparatively little about how OMVs are formed. Building upon the discovery that the Pseudomonas Quinolone Signal (PQS) stimulates OMV biogenesis in Pseudomonas aeruginosa, we proposed a model where PQS interacts with the outer membrane to induce curvature and ultimately OMV formation. Though this model is well supported in P. aeruginosa, it remained unclear whether other organisms produce similar compounds. Here we describe the development of a tightly controlled experimental system to test the interaction of bacterially-produced factors with target cells. Using this system, we show that multiple species respond to PQS by increasing OMV formation, that PQS accumulates in the induced vesicles, and that other bacteria secrete OMV-promoting factors. Analysis of induced vesicles indicates that recipient-mediated mechanisms exist to control vesicle size and that relatedness to the producer organism can dictate susceptibility to OMV-inducing compounds. This work provides evidence that small molecule induced OMV biogenesis is a widely conserved process and that cross-talk between systems may influence OMV production in neighboring bacteria.

Nitric Oxide, an Old Molecule With Noble Functions in Pseudomonas aeruginosa Biology

Pseudomonas aeruginosa, a Gram-negative bacterium, is characterized by its versatility that enables persistent survival under adverse conditions. It can grow on diverse energy sources and readily acquire resistance to antimicrobial agents. As an opportunistic human pathogen, it also causes chronic infections inside the anaerobic mucus airways of cystic fibrosis patients. As a strict respirer, P. aeruginosa can grow by anaerobic nitrate ( [Formula: see text] ) respiration. Nitric oxide (NO) produced as an intermediate during anaerobic respiration exerts many important effects on the biological characteristics of P. aeruginosa. This review provides information regarding (i) how P. aeruginosa grows by anaerobic respiration, (ii) mechanisms by which NO is produced under such growth, and (iii) bacterial adaptation to NO. We also review the clinical relevance of NO in the fitness of P. aeruginosa and the use of NO as a potential therapeutic for treating P. aeruginosa infection.

A quinolinol-based small molecule with anti-MRSA activity that targets bacterial membrane and promotes fermentative metabolism

In a loss-of-viability screen of small molecules against methicillin resistant S. aureus (MRSA) USA300, we found a small molecule, designated DNAC-2, which has an MIC of 8 μg/ml. DNAC-2 is a quinolinol derivative that is bactericidal at 2X MIC. Macromolecular synthesis assays at 2X MIC of DNAC-2 inhibited DNA, cell wall, RNA and protein synthesis within fifteen to thirty minutes of treatment when compared to the untreated control. Transmission electron microscopy of DNAC-2 treated cells revealed a significantly thicker cell wall and impaired daughter cell separation. Exposure of USA300 cells to 1X MIC of DNAC-2 resulted in mislocalization of PBP2 away from the septum in an FtsZ independent manner. In addition, membrane localization with FM4-64, as well as depolarization study with DiOC₂ and lipophilic cation TPP+ displayed membrane irregularities and rapid membrane depolarization in DNAC-2 treated cells vs. untreated control. However, DNAC-2 exhibited almost no toxicity towards eukaryotic membranes. Notably, DNAC-2 drives energy generation towards substrate level phosphorylation and the bacteria become more sensitive to DNAC-2 under anaerobic conditions. We propose that DNAC-2 affects USA300 by targeting the membrane, leading to partial membrane depolarization and subsequently affecting aerobic respiration and energy-dependent functional organization of macromolecular biosynthetic pathways. The multiple effects may have the desirable consequence of limiting the emergence of resistance to DNAC-2.

Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1

Many bacteria communicate with each other through signalling molecules, a process known as cell-to-cell communication. During this process, it is important for the signalling molecules to: (1) reach the target cells; and (2) to be received by the cognate receptor. Barriers such as the presence of extracellular matrix may prevent signals from reaching their targets; however, the influence of the extracellular matrix on cell-to-cell communication has scarcely been studied. Here, we demonstrate that the overproduction of an extracellular matrix, alginate, in a Pseudomonas aeruginosa mucoid variant, alters cell-to-cell communication by interfering with the response to quinolone signals while having no effect on N-acyl-L-homoserine lactones. The inhibition of quinolone signalling by alginate is limited to the alginate overproducer and has no effect on neighbour cells that do not produce alginate. Our study indicates that alginate overproduction affects the cell-to-cell communication of the mucoid variant, which may results in different downstream behaviours when it emerges in the presence of the wild-type (WT).

Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response

In vitro studies of Pseudomonas aeruginosa and other pathogenic bacteria in biofilm aggregates have yielded detailed insight into their potential growth modes and metabolic flexibility under exposure to gradients of substrate and electron acceptor. However, the growth pattern of P. aeruginosa in chronic lung infections of cystic fibrosis (CF) patients is very different from what is observed in vitro, for example, in biofilms grown in flow chambers. Dense in vitro biofilms of P. aeruginosa exhibit rapid O₂ depletion within <50-100 μm due to their own aerobic metabolism. In contrast, in vivo investigations show that P. aeruginosa persists in the chronically infected CF lung as relatively small cell aggregates that are surrounded by numerous PMNs, where the activity of PMNs is the major cause of O₂ depletion rendering the P. aeruginosa aggregates anoxic. High levels of nitrate and nitrite enable P. aeruginosa to persist fueled by denitrification in the PMN-surrounded biofilm aggregates. This configuration creates a potentially long-term stable ecological niche for P. aeruginosa in the CF lung, which is largely governed by slow growth and anaerobic metabolism and enables persistence and resilience of this pathogen even under the recurring aggressive antimicrobial treatments of CF patients. As similar slow growth of other CF pathogens has recently been observed in endobronchial secretions, there is now a clear need for better in vitro models that simulate such in vivo growth patterns and anoxic microenvironments in order to help unravel the efficiency of existing or new antimicrobials targeting anaerobic metabolism in P. aeruginosa and other CF pathogens. We also advocate that host immune responses such as PMN-driven O₂ depletion play a central role in the formation of anoxic microniches governing bacterial persistence in other chronic infections such as chronic wounds.

Performance of the dominant bacterial species and microbial community in autotrophic denitrification coupled with iron cycle in immobilized systems

We used three stable reactors to investigate the rates of nitrate removal coupled with iron cycle and the subsequent influence of the reaction on bacterial communities. The iron-reducing bacterium Klebsiella sp. FC61 was immobilized on the reactor columns of the experimental groups B (only Klebsiella) and C (Klebsiella+magnetite). With the fluctuation of Fe²⁺ to Fe3⁺ (iron cycle), the average nitrate removal efficiency increased from 73.22% to 93.91% and 86.92% to 97.84% in groups B and C, respectively, as the influent nitrate concentration decreased from 40 to 10mg/L. However, the average rate of nitrate removal showed the opposite trend (from 2.08mg/L/h to 0.67mg/L/h and 2.41mg/L/h to 0.69mg/L/h in groups B and C, respectively) as the influent nitrate concentration decreased. Analysis of microbial distribution and community structures indicated that the population of Klebsiella sp. increased in groups B (from 18.21% to 41.21%) and C (from 25.43% to 46.80%) and contributed to the effective removal of nitrate in the reactors.

Effects of exogenous short-chain N-acyl homoserine lactone on denitrifying process of Paracoccus denitrificans

N-acyl-homoserine lactones (AHLs) serve as quorum-sensing signals, which control a number of bacterial processes in many proteobacteria. Here we report the effects of exogenous short-chain AHL on the denitrifying process of Paracoccus denitrificans, which are capable of aerobic and anaerobic growth by utilizing nitrate. The denitrification activity of these cells was monitored by measuring denitrification products (including nitrate, nitrite, and nitrous oxide), and the individual messenger ribonucleic acid (mRNA) levels of nitrate, nitrite, nitric oxide and nitrous oxide reductases. The results indicated that 2μmol/L C6-homoserine lactone (HSL) has little effect on cell density under either anaerobic or aerobic culture conditions, and the nitrate reduction activity appeared slightly affected by N-hexanoyl-DL-homoserine lactone (C6-HSL). However, exogenous C6-HSL significantly affected the transcription of nitrite reductase and nitric oxide reductase genes in P. denitrificans regardless of the presence of oxygen, and N₂O accumulation activity in P. denitrificans was suppressed by C6-HSL under aerobic condition. In contrast, exogenous C6-HSL stimulated the production of N₂O under anaerobic condition, suggesting that the regulation of denitrification by quorum sensing may be important in N₂O release.

Distal and proximal promoters co-regulate pqsR expression in Pseudomonas aeruginosa

The ubiquitous bacterium Pseudomonas aeruginosa is an opportunistic pathogen that can cause serious infections in immunocompromised individuals. P. aeruginosa virulence is controlled partly by intercellular communication, and the transcription factor PqsR is a necessary component in the P. aeruginosa cell-to-cell signaling network. PqsR acts as the receptor for the Pseudomonas quinolone signal, and it controls the production of 2-alkyl-4-quinolone molecules which are important for pathogenicity. Previous studies showed that the expression of pqsR is positively controlled by the quorum-sensing regulator LasR, but it was unclear how LasR is able to induce pqsR transcription. In this report, we further investigated the control of pqsR, and discovered two separate promoter sites that contribute to pqsR expression. LasR-mediated activation occurs at the distal promoter site, but this activation can be antagonized by the regulator CysB. The proximal promoter site also contributes to pqsR transcription, but initiation at this site is inhibited by a negative regulatory sequence element, and potentially by the H-NS family members MvaT and MvaU. We propose a model where positive and negative regulatory influences at each promoter site are integrated to modify pqsR expression. This arrangement could allow for information from both environmental signals and cell-to-cell communication to influence PqsR levels.

Unravelling the Genome-Wide Contributions of Specific 2-Alkyl-4-Quinolones and PqsE to Quorum Sensing in Pseudomonas aeruginosa

The pqs quorum sensing (QS) system is crucial for Pseudomonas aeruginosa virulence both in vitro and in animal models of infection and is considered an ideal target for the development of anti-virulence agents. However, the precise role played by each individual component of this complex QS circuit in the control of virulence remains to be elucidated. Key components of the pqs QS system are 2-heptyl-4-hydroxyquinoline (HHQ), 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), the transcriptional regulator PqsR and the PQS-effector element PqsE. To define the individual contribution of each of these components to QS-mediated regulation, transcriptomic analyses were performed and validated on engineered P. aeruginosa strains in which the biosynthesis of 2-alkyl-4-quinolones (AQs) and expression of pqsE and pqsR have been uncoupled, facilitating the identification of the genes controlled by individual pqs system components. The results obtained demonstrate that i) the PQS biosynthetic precursor HHQ triggers a PqsR-dependent positive feedback loop that leads to the increased expression of only the pqsABCDE operon, ii) PqsE is involved in the regulation of diverse genes coding for key virulence determinants and biofilm development, iii) PQS promotes AQ biosynthesis, the expression of genes involved in the iron-starvation response and virulence factor production via PqsR-dependent and PqsR-independent pathways, and iv) HQNO does not influence transcription and hence does not function as a QS signal molecule. Overall this work has facilitated identification of the specific regulons controlled by individual pqs system components and uncovered the ability of PQS to contribute to gene regulation independent of both its ability to activate PqsR and to induce the iron-starvation response.

Many bacterial pathogens control virulence gene expression and the development of antibiotic-resistant biofilms via intercellular communication through ‘quorum sensing’ (QS). QS systems depend on the synthesis, secretion and perception of diffusible signalling molecules that enable bacteria to synchronize their behaviour at the population level and are considered ideal targets for the development of anti-virulence drugs. Pseudomonas aeruginosa employs several overlapping QS circuits including the pqs system to control the expression of virulence determinants. The pqs QS system relies on multiple 2-alkyl-4-quinolones (AQs), including the Pseudomonas Quinolone Signal (PQS), as signal molecules. However, the individual contributions of key AQs and the effector proteins PqsR and PqsE within the auto-regulated pqs system have not been elucidated because of their inter-dependence. By constructing P. aeruginosa strains with multiple mutations in the pqs system and determining their transcriptomes in the presence or absence of PqsR, PqsE or exogenously supplied AQs, we define the distinct regulons involved and characterize a novel PQS signalling pathway independent of PqsR and the iron-starvation response.

Charcoal Disrupts Soil Microbial Communication through a Combination of Signal Sorption and Hydrolysis

The presence of charcoal in soil triggers a range of biological effects that are not yet predictable, in part because it interferes with the functioning of chemical signals that microbes release into their environment to communicate. We do not fully understand the mechanisms by which charcoal alters the biologically available concentrations of these intercellular signals. Recently, charcoal has been shown to sorb the signaling molecules that microbes release, rendering them ineffective for intercellular communication. Here, we investigate a second, potentially more important mechanism of interference: signaling-molecule hydrolysis driven by charcoal-induced soil pH changes. We examined the effects of 10 charcoals on the bioavailable concentration of an acyl-homoserine lactone (AHL) used by many Gram-negative bacteria for cell-cell communication. We show that charcoals decrease the level of bioavailable AHL through sorption and pH-dependent hydrolysis of the lactone ring. We then built a quantitative model that predicts the half-lives of different microbial signaling compounds in the presence of charcoals varying in pH and surface area. Our model results suggest that the chemical effects of charcoal on pH-sensitive bacterial AHL signals will be fundamentally distinct from effects on pH-insensitive fungal signals, potentially leading to shifts in microbial community structures.

Quantification and enzyme targets of fatty acid amides from duckweed root exudates involved in the stimulation of denitrification

Fatty acid amides from plant root exudates, such as oleamide and erucamide, have the ability to participate in strong plant-microbe interactions, stimulating nitrogen metabolism in rhizospheric bacteria. However, mechanisms of secretion of such fatty acid amides, and the nature of their stimulatory activities on microbial metabolism, have not been examined. In the present study, collection, pre-treatment, and determination methods of oleamide and erucamide in duckweed root exudates are compared. The detection limits of oleamide and erucamide by gas chromatography (GC) (10.3ngmL(-1) and 16.1ngmL(-1), respectively) are shown to be much lower than those by liquid chromatography (LC) (1.7 and 5.0μgmL(-1), respectively). Quantitative GC analysis yielded five times larger amounts of oleamide and erucamide in root exudates of Spirodela polyrrhiza when using a continuous collection method (50.20±4.32 and 76.79±13.92μgkg(-1) FW day(-1)), compared to static collection (10.88±0.66 and 15.27±0.58μgkg(-1) FW day(-1)). Furthermore, fatty acid amide secretion was significantly enhanced under elevated nitrogen conditions (>300mgL(-1)), and was negatively correlated with the relative growth rate of duckweed. Mechanistic assays were conducted to show that erucamide stimulates nitrogen removal by enhancing denitrification, targeting two key denitrifying enzymes, nitrate and nitrite reductases, in bacteria. Our findings significantly contribute to our understanding of the regulation of nitrogen dynamics by plant root exudates in natural ecosystems.

Origin and Impact of Nitric Oxide in Pseudomonas aeruginosa Biofilms

The formation of the organized bacterial community called biofilm is a crucial event in bacterial physiology. Given that biofilms are often refractory to antibiotics and disinfectants to which planktonic bacteria are susceptible, their formation is also an industrially and medically relevant issue. Pseudomonas aeruginosa, a well-known human pathogen causing acute and chronic infections, is considered a model organism to study biofilms. A large number of environmental cues control biofilm dynamics in bacterial cells. In particular, the dispersal of individual cells from the biofilm requires metabolic and morphological reprogramming in which the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) plays a central role. The diatomic gas nitric oxide (NO), a well-known signaling molecule in both prokaryotes and eukaryotes, is able to induce the dispersal of P. aeruginosa and other bacterial biofilms by lowering c-di-GMP levels. In this review, we summarize the current knowledge on the molecular mechanisms connecting NO sensing to the activation of c-di-GMP-specific phosphodiesterases in P. aeruginosa, ultimately leading to c-di-GMP decrease and biofilm dispersal.

Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms

Many bacteria produce extracellular and surface-associated components such as membrane vesicles (MVs), extracellular DNA and moonlighting cytosolic proteins for which the biogenesis and export pathways are not fully understood. Here we show that the explosive cell lysis of a sub-population of cells accounts for the liberation of cytosolic content in Pseudomonas aeruginosa biofilms. Super-resolution microscopy reveals that explosive cell lysis also produces shattered membrane fragments that rapidly form MVs. A prophage endolysin encoded within the R- and F-pyocin gene cluster is essential for explosive cell lysis. Endolysin-deficient mutants are defective in MV production and biofilm development, consistent with a crucial role in the biogenesis of MVs and liberation of extracellular DNA and other biofilm matrix components. Our findings reveal that explosive cell lysis, mediated through the activity of a cryptic prophage endolysin, acts as a mechanism for the production of bacterial MVs.