Pressure-dependent growth controls 3D architecture of Pseudomonas putida microcolonies

Colony formation is key to many ecological and biotechnological processes. In its early stages, colony formation involves the concourse of a number of physical and biological parameters for generation of a distinct 3D structure-the specific influence of which remains unclear. We focused on a thus far neglected aspect of the process, specifically the consequences of the differential pressure experienced by cells in the middle of a colony versus that endured by bacteria located in the growing periphery. This feature was characterized experimentally in the soil bacterium Pseudomonas putida. Using an agent-based model we recreated the growth of microcolonies in a scenario in which pressure was the only parameter affecting proliferation of cells. Simulations exposed that, due to constant collisions with other growing bacteria, cells have virtually no free space to move sideways, thereby delaying growth and boosting chances of overlapping on top of each other. This scenario was tested experimentally on agar surfaces. Comparison between experiments and simulations suggested that the inside/outside differential pressure determines growth, both timewise and in terms of spatial directions, eventually moulding colony shape. We thus argue that-at least in the case studied-mere physical pressure of growing cells suffices to explain key dynamics of colony formation.

Aedes aegypti Toll pathway is induced through dsRNA sensing in endosomes

Mosquito anti-pathogen immune responses, including those controlling infection with arboviruses are regulated by multiple signal transduction pathways. While the Toll pathway is critical in the defense against arboviruses such as dengue and Zika viruses, the factors and mechanisms involved in virus recognition leading to the activation of the Toll pathway are not fully understood. In this study we evaluated the role of virus-produced double-stranded RNA (dsRNA) intermediates in mosquito immune activation by utilizing the synthetic dsRNA analog polyinosinic-polycytidylic acid (poly I:C). Poly I:C treatment of Aedes aegypti mosquitoes and Aag2 cells reduced DENV infection. Transcriptomic analyses of Aag2 cell responses to poly I:C indicated putative activation of the Toll pathway. We found that poly I:C is translocated to the endosomal compartment of Aag2 cells, and that the A. aegypti Toll 6 receptor is a putative dsRNA recognition receptor. This study elucidates the role of dsRNAs in the immune activation of non-RNAi pathways in mosquitoes.

Transformation of Iodosulfuron-Methyl into Ionic Liquids Enables Elimination of Additional Surfactants in Commercial Formulations of Sulfonylureas

Efficient use of herbicides for plant protection requires the application of auxiliary substances such as surfactants, stabilizers, wetting or anti-foaming agents, and absorption enhancers, which can be more problematic for environment than the herbicides themselves. We hypothesized that the combination of sulfonylurea (iodosulfuron-methyl) anion with inexpensive, commercially available quaternary tetraalkylammonium cations could lead to biologically active ionic liquids (ILs) that could become a convenient and environment-friendly alternative to adjuvants. A simple one-step synthesis allowed for synthesizing iodosulfuron-methyl based ILs with high yields ranging from 88 to 96% as confirmed by UV, FTIR, and NMR. The obtained ILs were found to possess several favorable properties compared to the currently used sodium salt iodosulfuron-methyl, such as adjustable hydrophobicity (octanol-water partition coefficient) and enhanced stability in aqueous solutions, which was supported by molecular calculations showing cation-anion interaction energies. In addition, soil mobility and volatility of ILs were more beneficial compared to the parental herbicide. Herbicidal activity tests toward oil-seed rape and cornflower revealed that ILs comprising at least one alkyl chain in the decyl to octadecyl range had similar or better efficacy compared to the commercial preparation without addition of any adjuvant. Furthermore, results of antimicrobial activity indicated that they were practically harmless or slightly toxic toward model soil microorganisms such as Pseudomonas putida and Bacillus cereus.

An Exploration of Seaweed Polysaccharides Stimulating Denitrifying Bacteria for Safer Nitrate Removal

Excessive use of nitrogen fertilizer in intensively managed agriculture has resulted in abundant accumulation of nitrate in soil, which limits agriculture sustainability. How to reduce nitrate content is the key to alleviate secondary soil salinization. However, the microorganisms used in soil remediation cause some problems such as weak efficiency and short survival time. In this study, seaweed polysaccharides were used as stimulant to promote the rapid growth and safer nitrate removal of denitrifying bacteria. Firstly, the growth rate and NO₃⁻-N removal capacity of three kinds of denitrifying bacteria, Bacillus subtilis (BS), Pseudomonas stutzeri (PS) and Pseudomonas putida (PP), were compared. The results showed that Bacillus subtilis (BS) had a faster growth rate and stronger nitrate removal ability. We then studied the effects of Enteromorpha linza polysaccharides (EP), carrageenan (CA), and sodium alginate (AL) on growth and denitrification performance of Bacillus subtilis (BS). The results showed that seaweed polysaccharides obviously promoted the growth of Bacillus subtilis (BS), and accelerated the reduction of NO₃⁻-N. More importantly, the increased NH₄⁺-N content could avoid excessive loss of nitrogen, and less NO₂⁻-N accumulation could avoid toxic effects on plants. This new strategy of using denitrifying bacteria for safely remediating secondary soil salinization has a great significance.

Temperature regulation as a tool to program synthetic microbial community composition

Engineering of synthetic microbial communities is emerging as a powerful new paradigm for performing various industrially, medically, and environmentally important processes. To reach the fullest potential, however, this approach requires further development in many aspects, a key one being regulating the community composition. Here we leverage well-established mechanisms in ecology which govern the relative abundance of multispecies ecosystems and develop a new tool for programming the composition of synthetic microbial communities. Using a simple model system consisting of two microorganisms Escherichia coli and Pseudomonas putida, which occupy different but partially overlapping thermal niches, we demonstrated that temperature regulation could be used to enable coexistence and program the community composition. We first investigated a constant temperature regime and showed that different temperatures led to different community compositions. Next, we invented a new cycling temperature regime and showed that it can dynamically tune the microbial community, achieving a wide range of compositions depending on parameters that are readily manipulatable. Our work provides conclusive proof of concept that temperature regulation is a versatile and powerful tool capable of programming compositions of synthetic microbial communities.

Role of bacterial cell surface sulfhydryl sites in cadmium detoxification by Pseudomonas putida

Understanding bacterial metal detoxification systems is crucial for determining the environmental impacts of metal pollution and for developing advanced bioremediation and water disinfection strategies. Here, we explore the role of cell surface sulfhydryl sites in bacterial detoxification of Cd, using Pseudomonas putida with surface sulfhydryl sites mostly on its EPS molecules as a model organism. Our results show that 5 and 20 ppm Cd in LB growth medium affects the lag phase of P. putida, but not the overall extent of cell growth at stationary phase, indicating that P. putida can detoxify Cd at these concentrations. EXAFS analysis of Cd bound to biomass from the different growth stages indicates that Cd binds to both sulfhydryl and non-sulfhydryl sites, but that the importance of Cd-sulfhydryl binding increases from early exponential to stationary phase. Cell growth is positively correlated to the measured sulfhydryl concentration on different biomass samples, but is independent of the measured non-sulfhydryl binding site concentration on the cell surfaces. Taken together, our results demonstrate that the sulfhydryl binding sites on EPS molecules can play an important role in binding and detoxifying toxic metals, significantly decreasing the bioavailability of the metal by sequestering it away from the bacterial cells.

Parameter identification for gompertz and logistic dynamic equations

In this paper, we generalize and compare Gompertz and Logistic dynamic equations in order to describe the growth patterns of bacteria and tumor. First of all, we introduce two types of Gompertz equations, where the first type 4-paramater and 3-parameter Gompertz curves do not include the logarithm of the number of individuals, and then we derive 4-parameter and 3-parameter Logistic equations. We notice that Logistic curves are better in modeling bacteria whereas the growth pattern of tumor is described better by Gompertz curves. Increasing the number of parameters of Logistic curves give favorable results for bacteria while decreasing the number of parameters of Gompertz curves for tumor improves the curve fitting. Moreover, our results overshadow some of the existing results in the literature.

Towards a better understanding of Pseudomonas putida biofilm formation in the presence of ZnO nanoparticles (NPs): Role of NP concentration

Elucidating the effects of nanoparticles (NPs) on key bacterial functions not only deepens our understanding of nano-toxicity mechanisms, but also guides us in the design criteria for manufacturing safe nanomaterials. In this study, bacterial growth, biofilm development and the expression of biofilm-related genes were monitored in Pseudomonas putida KT2440, a plant-beneficial bacterium, following exposure to ZnO NPs. Low concentrations of NPs (0.5-30 mg L^-1) significantly promoted bacterial growth and biofilm formation, while higher concentrations (>30 mg L^-1) significantly inhibited biofilm formation. Confocal laser scanning microscopy revealed that microscope slides coated with 0.5 mg L^-1 of ZnO NPs showed enhanced bacterial colonization and biomass production, but at higher concentrations (250 mg L^-1), biomass production was about 11 times lower than that of the substrate without NPs. Increased protein and sugar contents of the biofilm matrix corroborated the stimulating effects of low concentrations of ZnO NPs. Physiological data were supported by changes in the expression of genes associated with oxidative stress and biofilm development. ZnO NPs at 0.5 mg L^-1 stimulated the expression of quorum sensing, lipopolysaccharide biosynthesis, and antibiotic resistance genes; high concentrations of ZnO NPs (250 mg L^-1) down-regulated biofilm formation-related genes and up-regulated antioxidant genes. Our results indicate that long-term release of low concentrations of ZnO NPs to the environment would promote undesired biofilm formation and increased resistance to antibiotics.

Synergistic effect of Pseudomonas putida II-2 and Achromobacter sp. QC36 for the effective biodegradation of the herbicide quinclorac

Quinclorac (QNC) is an effective but environmentally persistent herbicide commonly used in rice production. However, few studies have investigated its environmental behavior and degradation. In the present study, we carried out microbial cultures in the presence of QNC to observe changes in soil microbiota and to identify species capable of QNC degradation by using high-throughput sequencing of the 16S rRNA. Pseudomonas was the dominant genus, and Pseudomonas putida II-2 and other species were found to be capable of mineralizing QNC as a source of carbon and energy. However, this degradation rate was slow, only reaching 51.5 ± 1.6% for 7 days at 30 °C on QNC + minimal salt medium. Achromobacter sp. QC36 co-metabolized QNC when rice straw was added into the mineral salt medium containing QNC, and a mixed culture of both strains could mineralize approximately 92% of the 50 mg/L QNC after 5 days of cultivation in the presence of rice straw, at 25-35 °C and pH 6.0-8.0. Non-phytotoxicity of tobacco after degradation of QNC by mixed strains was evidenced in a pot experiment. These results suggest that this mixed culture may be useful in QNC bioremediation and can be used as a bio-formulation for agro-economical and industrial application.

Optimization of plant hormonal balance by microorganisms prevents plant heavy metal accumulation

Heavy metal contamination is a threat to global food safety. Reducing heavy metal uptake in plants is a promising way to make plants safer, yet breeding the right set of traits can be tedious. We test whether microorganisms are able to impact the plant's hormonal balance hereby helping to manage plant heavy metal uptake. We focus on ethylene, a plant hormone regulating plant stress tolerance and nutrition. We grew three phylogenetically distinct plants, Rumex palustris, Alcea aucheri and Arabidopsis thaliana, on a cadmium-spiked soil. Plants roots were coated with the bacterium Pseudomonas putida UW4, which degrades the precursor of ethylene, or an isogenic ACC deaminase-deficient mutant lacking this ability. We followed ethylene concentrations, plant growth and cadmium uptake. Wildtype bacteria reduced shoot cadmium concentration by up to 35% compared to the control, while the mutant increased cadmium concentration. This effect was linked to ethylene, which was consistently positively correlated with cadmium concentration. We therefore propose that bacteria modulating plant hormonal balance may offer new possibilities to improve specific aspects of plant phenotype, in the present context reducing heavy metal. They may thus pave the way for new strategies to improve food safety in a context of the widespread soil contamination.

Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium

When the soil bacterium Pseudomonas putida grows in a complete medium, it prioritizes the assimilation of preferred carbon sources, optimizing its metabolism and growth. This regulatory process is orchestrated by the Crc and Hfq proteins. The present work examines the changes that occur in metabolic fluxes when the crc gene is inactivated and cells grow exponentially in LB complete medium. Analyses were performed at three different moments during exponential growth, examining the assimilation rates for the compounds present in LB, changes in the proteome, and the changes in metabolic fluxes predicted by the iJN1411 metabolic model for P. putida KT2440. During the early exponential phase, consumption rates for sugars, many organic acids and most amino acids were higher in a Crc-null strain than in the wild type, leading to an overflow of the metabolic pathways and the leakage of pyruvate and acetate. These accelerated consumption rates decreased during the mid-exponential phase, when cells mostly used sugars and alanine. At later times, pyruvate was recovered from the medium and utilized. The higher consumption rates of the Crc-null strain reduced the growth rate. The lack of the Crc/Hfq regulatory system thus led to unbalanced metabolism with poorly optimized metabolic fluxes.

Effective biodegradation of pentachloronitrobenzene by a novel strain Peudomonas putida QTH3 isolated from contaminated soil

To eliminate pentachloronitrobenzene (PCNB) residue in PCNB-contaminated environment, the degradation potential of Pseudomonas putida QTH3 to PCNB was evaluated in this study. Peudomonas putida QTH3 could grow well in mineral salt medium (MSM) containing PCNB as sole carbon and was able to degrade PCNB efficiently, whereas the degradation rate of P. putida QTH3 to PCNB increased gradually, and reached 49.84% in 35 days. The degradation rates of P. putida QTH3 to 13 tested organochlorine compounds found to be 10.85%-42.51% after 14 days. The metabolites during PCNB biodegradation by P. putida QTH3 were identified as catechol, 2, 3, 5, 6-tetrachloroaniline (TCA), 2, 3, 4, 5- TCA, 2, 3, 4, 5, 6-pentachloroaniline (PCA) and pentachlorothioanisole (PCTAs). Furthermore, possible degradation pathway of PCNB by P. putida QTH3 was proposed. The degradation rates of intracellular enzyme and extracellular enzyme were 44.73% and 8.93% after incubation with 100 mg L^-1 PCNB for 30 min, respectively. Thus, intracellular enzyme is a major enzyme responsible for PCNB degradation. The results indicate that P. putida QTH3 can be a suitable organism for the degradation of PCNB, and facilitate its potential for the bioremediation of the environments contaminated with major organochlorine compounds used during this study.

Segregostat: a novel concept to control phenotypic diversification dynamics on the example of Gram-negative bacteria

Controlling and managing the degree of phenotypic diversification of microbial populations is a challenging task. This task not only requires detailed knowledge regarding diversification mechanisms but also advanced technical set-ups for the real-time analyses and control of population behaviour on single-cell level. In this work, set-up, design and operation of the so called segregostat are described which, in contrast to a traditional chemostat, allows the control of phenotypic diversification of microbial populations over time. Two exemplary case studies will be discussed, i.e. phenotypic diversification dynamics of Eschericia coli and Pseudomonas putida based on outer membrane permeabilization, emphasizing the applicability and versatility of the proposed approach. Upon nutrient limitation, cell population tends to diversify into several subpopulations exhibiting distinct phenotypic features (non-permeabilized and permeabilized cells). Online analysis leads to the determination of the ratio between cells in these two states, which in turn triggers the addition of glucose pulses in order to maintain a predefined diversification ratio. These results prove that phenotypic diversification can be controlled by means of defined pulse-frequency modulation within continuously running bioreactor set-ups. This lays the foundation for systematic studies, not only of phenotypic diversification but also for all processes where dynamics single-cell approaches are required, such as synthetic co-culture processes.

Pseudomonas putida KT2440 is HV1 certified, not GRAS

Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.

Cell density-dependent auto-inducible promoters for expression of recombinant proteins in Pseudomonas putida

Inducible promoters such as Plac are of limited usability for industrial protein production with Pseudomonas putida. We therefore utilized cell density-dependent auto-inducible promoters for recombinant gene expression in P. putida KT2440 based on the RoxS/RoxR Quorum Sensing (QS) system of the bacterium. To this end, genetic regions upstream of the RoxS/RoxR-regulated genes ddcA (PR ox132 ) and PP_3332 (PR ox306 ) were inserted into plasmids that mediated the expression of superfolder green fluorescent protein (sfGFP) and surface displayed mCherry, confirming their promoter functionalities. Mutation of the Pribnow box of PR ox306 to the σ70 consensus sequence (PR ox3061 ) resulted in a more than threefold increase of sfGFP production. All three promoters caused cell density-dependent expression, starting transcription at optical densities (OD578 ) of approximately 1.0 (PR ox132 , PR ox306 ) or 0.7 (PR ox3061 ) as determined by RT-qPCR. The QS dependency of PR ox306 was further shown by cultivating P. putida in media that had already been used for cultivation and thus contained bacterial signal molecules. The longer P. putida had grown in these media before, the earlier protein expression in freshly inoculated P. putida appeared with PR ox306 . This confirmed previous findings that a bacterial compound accumulates within the culture and induces protein expression.

Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

Pseudomonas putida is widely used as a biocontrol agent, however, mechanisms by which it initiates the plants' defense response remains obscure. To gain an insight into the molecular changes that occur in plants upon plant growth-promoting rhizobacteria colonization, root transcriptome analysis by using a microarray was performed in rice using P. putida RRF3 (a rice rhizosphere isolate). Data analysis revealed a differential regulation of 61 transcripts (48 h post-treatment), of which, majority corresponded to defense response, cell wall modification and secondary metabolism. Seven genes encoding salicylic acid (SA) responsive pathogenesis-related proteins were up-regulated significantly (fold change ranges from 1 to 4), which suggests that RRF3 has a profound impact on a SA-mediated defense signaling mechanism in rice. Investigations performed at later stages of RRF3 colonization by real-time polymerase chain reaction and high-performance liquid chromatography (HPLC) analysis confirmed the above results, demonstrating RRF3 as a potent biocontrol agent. Further, the impact of RRF3 colonization on root exudation, in particular, exudation of SA was investigated by HPLC. However, analysis revealed RRF3 to have a negative impact on root exudation of SA. Overall, this study shows that P. putida RRF3 immunizes the rice plants by re-organizing the root transcriptome to stimulate plant defense responses ('priming'), and simultaneously protects itself from the primed plants by altering the rhizosphere chemical constituents.

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.

An automated and parallelised DIY-dosing unit for individual and complex feeding profiles: Construction, validation and applications

Since biotechnological research becomes more and more important for industrial applications, there is an increasing need for scalable and controllable laboratory procedures. A widely used approach in biotechnological research to improve the performance of a process is to vary the growth rates in order to find the right balance between growth and the production. This can be achieved by the application of a suitable feeding strategy. During this initial bioprocess development, it is beneficial to have at hand cheap and easy setups that work in parallel (e.g. in shaking flasks). Unfortunately, there is a gap between these easy setups and defined and controllable processes, which are necessary for up-scaling to an industrial relevant volume. One prerequisite to test and evaluate different process strategies apart from batch-mode is the availability of pump systems that allow for defined feeding profiles in shaking flasks. To our knowledge, there is no suitable dosing device on the market which fulfils the requirements of being cheap, precise, programmable, and parallelizable. Commercially available dosing units are either already integrated in bioreactors and therefore inflexible, or not programmable, or expensive, or a combination of those. Here, we present a LEGO-MINDSTORMS-based syringe pump, which has the potential of being widely used in daily laboratory routine due to its low price, programmability, and parallelisability. The acquisition costs do not exceed 350 € for up to four dosing units, that are independently controllable with one EV3 block. The system covers flow rates ranging from 0.7 μL min-1 up to 210 mL min-1 with a reliable flux. One dosing unit can convey at maximum a volume of 20 mL (using all 4 units even up to 80 mL in total) over the whole process time. The design of the dosing unit enables the user to perform experiments with up to four different growth rates in parallel (each measured in triplicates) per EV3-block used. We estimate, that the LEGO-MINDSTORMS-based dosing unit with 12 syringes in parallel is reducing the costs up to 50-fold compared to a trivial version of a commercial pump system (~1500 €) which fits the same requirements. Using the pump, we set the growth rates of a E. coli HMS174/DE3 culture to values between 0.1 and 0.4 h-1 with a standard deviation of at best 0.35% and an average discrepancy of 13.2%. Additionally, we determined the energy demand of a culture for the maintenance of the pTRA-51hd plasmid by quantifying the changes in biomass yield with different growth rates set. Around 25% of total substrate taken up is used for plasmid maintenance. To present possible applications and show the flexibility of the system, we applied a constant feed to perform microencapsulation of Pseudomonas putida and an individual dosing profile for the purification of a his-tagged eGFP via IMAC. This smart and versatile dosing unit, which is ready-to-use without any prior knowledge in electronics and control, is affordable for everyone and due to its flexibility and broad application range a valuable addition to the laboratory routine.

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling

Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modelling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.

PvdRT-OpmQ and MdtABC-OpmB efflux systems are involved in pyoverdine secretion in Pseudomonas putida KT2440

Fluorescent pseudomonads produce and secrete a siderophore termed pyoverdine to capture iron when it becomes scarce. The molecular basis of pyoverdine secretion is only partially understood. Here, we investigate the role of the putative PvdRT-OpmQ and MdtABC-OpmB efflux systems in pyoverdine secretion in the soil bacterium Pseudomonas putida KT2440. Expression from the respective promoters is stimulated by iron limitation albeit to varying degrees. Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation. Deletion of mdtABC-opmB does not affect growth. However, when both systems are deleted, strong effects on growth and pyoverdine secretion (yellow colony phenotype, less pyoverdine in medium, more pyoverdine in the periplasm) are observed. Overexpression of pvdRT-opmQ causes the opposite effect. These results provide first evidence for an involvement of the multidrug efflux system MdtABC-OpmB in pyoverdine secretion. In addition, the PvdRT-OpmQ system was shown to contribute to pyoverdine secretion in P. putida KT2440, extending previous investigations on its role in Pseudomonas species. Since the double deletion mutant still secrets pyoverdine, at least one additional efflux system participates in the transport of the siderophore. Furthermore, our results suggest a contribution of both efflux systems to ampicillin resistance.

Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System

Interactions among members of microbial consortia drive the complex dynamics in soil, gut, and biotechnology microbiomes. Proteomic analysis of defined co-cultures of well-characterized species provides valuable information about microbial interactions. We used a label-free approach to quantify the responses to co-culture of two model bacterial species relevant to soil and rhizosphere ecology, Bacillus atrophaeus and Pseudomonas putida. Experiments determined the ratio of species in co-culture that would result in the greatest number of high-confidence protein identifications for both species. The 281 and 256 proteins with significant shifts in abundance for B. atrophaeus and P. putida, respectively, indicated responses to co-culture in overall metabolism, cell motility, and response to antagonistic compounds. Proteins associated with a virulent phenotype during surface-associated growth were significantly more abundant for P. putida in co-culture. Co-culture on agar plates triggered a filamentous phenotype in P. putida and avoidance of P. putida by B. atrophaeus colonies, corroborating antagonistic interactions between these species. Additional experiments showing increased relative abundance of P. putida under conditions of iron or zinc limitation and increased relative abundance of B. atrophaeus under magnesium limitation were consistent with patterns of changes in abundance of metal-binding proteins during co-culture. These results provide details on the nature of interactions between two species with antagonistic capabilities. Significant challenges remaining for the development of proteomics as a tool in microbial ecology include accurate quantification of low-abundance peptides, especially from rare species present at low relative abundance in a consortium.

Antimicrobial and antibiofilm efficacy of self-cleaning surfaces functionalized by TiO2 photocatalytic nanoparticles against Staphylococcus aureus and Pseudomonas putida

A photocatalytic sol of TiO₂ nanoparticles has been used for creating self-cleaning antimicrobial flat and porous glass surfaces. The substrates were irradiated to study their photocatalytic properties and behavior in the presence of biofilm-forming bacteria. Smooth glass surfaces and glass microfiber filters were covered with 1.98×10^-3±1.5×10^-4gcm^-2 and 8.55×10^-3±3.0×10^-4gcm^-2 densities, respectively. Self-cleaning properties were analyzed using the methylene blue 365nm UV-A photodegradation test. TiO₂-coated filters achieved rapid and complete photodegradation of methylene blue because of the better TiO₂ dispersion with respect to the glass slides. The effect of functionalized surfaces on the growth and viability of bacteria was studied using the strains Staphylococcus aureus and Pseudomonas putida. After irradiation (2h, 11.2Wm^-2, 290-400nm), the initially hydrophobic surface turned hydrophilic. The antibacterial effect led to extensive membrane damage and significant production of intracellular reactive oxygen species in all TiO₂-loaded irradiated specimens. The reduction of cell viability was over 99.9% (>3-log) for TiO₂ on glass surfaces. However, the polymeric extracellular matrix formed before the irradiation treatment was not removed. This study highlights the importance of bacterial colonization during dark periods and the difficulty of removing the structure of biofilms.

Oxygen mass transfer and shear stress effects on Pseudomonas putida BCRC 14365 growth to improve bioreactor design and performance

In this work, the experimental evidence is presented for two basic issues including oxygen mass transfer and shear analysis on the microorganism containing medium on the most prominent sections of the bioreactor. Computational fluid dynamics (CFD) methodology reproduces shear rate values for specific impeller designs using the commercial code (Fluent 6.2). CFD calculates volumetric mass transfer coefficient based on the Higbie's penetration theory. Four types of impeller are used. The spherical probe is used to measure flow hydrodynamic parameters to obtain shear rate by electro-diffusion (ED) method. The obtained results are validated experimentally and it is shown that a fully axial pattern impeller represents more enhanced results than partially axial and radial. In this regard, experimental results for volumetric oxygen mass transfer coefficient (k _l a) confirm CFD predictions by acceptable deviations of 2.65, 8.90, and 9.20 for 0.15, 0.2, and 0.3 VVM, respectively. These results collaboratively indicate that LIGHTNIN-C 200 type operates more efficiently by reflecting the flow to the bottom corner stagnation areas with the minimum tolerable shear and the most velocity distribution uniformity. Furthermore, the values of k _l a improve by aeration rate. Conversely, increasing the rotational speed of impeller creates difficulties for cell growth due to the generated harsh shear condition. CFD provide a better understanding of how operational and geometrical variables may be manipulated to achieve a moderate shear rate and acceptable level of mass transfer.

FleN and FleQ play a synergistic role in regulating lapA and bcs operons in Pseudomonas putida KT2440

FleN generally functions as an antagonist of FleQ in regulating flagellar genes and biofilm matrix related genes in Pseudomonas aeruginosa. Here, we found that in Pseudomonas putida KT2440, FleN and FleQ play a synergistic role in regulating two biofilm matrix coding operons, lapA and bcs. FleN deletion decreased the transcription of lapA and increased the transcription of bcs operon, and the same trend was observed in fleQ deletion mutant before. In vitro experiments showed that FleN promoted the binding of FleQ to the lapA/bcs promoter DNA especially in the presence of ATP. Both phenotype observation and transcription analysis showed that, similar to fleQ deletion, fleN deletion significantly weaken the effect of high c-di-GMP level on biofilm formation, surface winkle phenotype and expression of lapA and bcs operons. Mutagenesis of the putative ATP binding motif in FleN_K21Q revealed that FleN ATPase activity played an essential role in the regulation of flagellar number and swimming motility but was not critical for biofilm formation. Our results revealed that FleN was not an antagonist of FleQ but a synergistic factor of FleQ in regulating the two biofilm matrix coding operons in P. putida KT2440.

Impact of the composition of the bacterial population and additional carbon source on the pathway and kinetics of degradation of endosulfan isomers

Abiotic and bacterial degradation is presented for the two isomers α- and β- of the organochlorine pesticide endosulfan, denoted as ES-1 and ES-2, respectively. Biodegradation studies were conducted with two indigenous species Pseudomonas putida (P. putida) and Rhodococcus sp. Both ES isomers rapidly hydrolyzed in water at pH ≥ 7 but the hydrolysis was inhibited in the presence of biomass. The pesticide partitioned onto the biomass making it unavailable for abiotic hydrolytic reaction. Spontaneous temperature dependent abiotic conversion of ES-2 to ES-1 was reported in the presence of dual air-water phases but was not observed in the abiotic aqueous phase. Biodegradation experiments with pure isomers showed a small amount of interconversion (∼5%) in either direction and ruled out any preferential interconversion of the ES-2 isomer to ES-1 or vice versa. Both the species were shown to degrade ES-2 at a higher rate compared to ES-1 which may lead to enrichment of ES-1 in agricultural fields in short-term following application of the pesticide. P. putida degraded both the ES isomers through oxidative and hydrolytic pathways while the Rhodococcus sp. used only the hydrolytic pathway. Since ES-S (product of the oxidative pathway) is orders of magnitude more toxic than the parent isomers, the short term toxicity of a field following the application of the pesticide may increase if the composition of the indigenous bacterial population is such that the oxidative pathway is preferred over the hydrolytic one. The presence of an additional carbon source increased the rates of degradation of both the isomers but the enhancement was greater for the degradation rate of ES-2 than ES-1.

Isotope fractionation associated with the simultaneous biodegradation of multiple nitrophenol isomers by Pseudomonas putida B2

Quantifying the extent of biodegradation of nitroaromatic compounds (NACs) in contaminated soils and sediments is challenging because of competing oxidative and reductive reaction pathways. We have previously shown that the stable isotope fractionation of NACs reveals the routes of degradation even if it is simultaneously caused by different bacteria. However, it is unclear whether compound-specific isotope analysis (CSIA) can be applied in situations where multiple pollutants are biodegraded by only one microorganism under multi-substrate conditions. Here we examined the C and N isotope fractionation of 2-nitrophenol (2-NP) and 3-nitrophenol (3-NP) during biodegradation by Pseudomonas putida B2 through monooxygenation and partial reductive pathways, respectively, in the presence of single substrates vs. binary substrate mixtures. Laboratory experiments showed that the reduction of 3-NP by Pseudomonas putida B2 is associated with large N and minor C isotope fractionation with C and N isotope enrichment factors, ε_C and ε_N, of -0.3 ± 0.1‰ and -22 ± 0.2‰, respectively. The opposite isotope fractionation trends were found for 2-NP monooxygenation. In the simultaneous presence of 2-NP and 3-NP, 2-NP is biodegraded at identical rate constants and ε_C and ε_N values (-1.0 ± 0.1‰ and -1.3 ± 0.2‰) to those found for the monooxygenation of 2-NP in single substrate experiments. While the pathway and N isotope fractionation of 3-NP reduction (ε_N = -24 ± 1.1‰) are independent of the presence of 2-NP, intermediates of 2-NP monooxygenation interfere with 3-NP reduction. Because neither pH, substrate uptake, nor aromatic substituents affected the kinetic isotope effects of nitrophenol biodegradation, our study illustrates that CSIA provides robust scientific evidence for the assessment of natural attenuation processes.

A facile approach for surface alteration of Pseudomonas putida I3 by supplying K2SO4 into growth medium: Enhanced removal of Pb(II) from aqueous solution

A new sight of obtaining a high efficient biosorbent by supplying specific salts into bacterial growth medium was investigated in this study for Pb(II). Among a series of salts including Na₂SO₄, Na₂S₂O₃, KCl, and K₂SO₄, the highest Pb(II) removal efficiency was observed by psychrotrophilic Pseudomonas putida I3 grown in the presence of 30g/L K₂SO₄ (KSI3-30) with biosorption capacity of 62.89mg/g under cold condition (15°C), which was increased by 42.35% as compared to control (without any additive, RI3). This stimulation effect was ascribed to the increase of potassium and sulfur containing groups on KSI3-30 surface via metabolic dependent ways. The probable mechanism for Pb(II) adsorption was ion-exchange and chemical complexation. The thermal and kinetic data well fitted to Langmuir adsorption model and pseudo-second order and intraparticle diffusion kinetic model. Good recyclability and effectively dealing with real wastewater suggested KSI3-30 was a promising biosorbent for Pb-contaminated wastewater treatment.

Toxicity evaluation of selected ammonium-based ionic liquid forms with MCPP and dicamba moieties on Pseudomonas putida

Combination of the hydrophilic herbicidal anion with hydrophobic, antimicrobial ammonium cation allows to obtain compounds in ionic liquid form with better properties then conventional herbicides. Both cation and anion can be modified by selection of herbicide and the length of alkyl chains in cation structure. However the knowledge of their potential toxic effects are still limited. Furthermore, the relation between hydrophobicity associated with the length of alkyl chains and toxicity for ionic liquids has not been thoroughly studied. Therefore we investigated toxic effects of herbicidal ionic liquid forms on growth inhibition, given as EC_50, of the common soil bacterium Pseudomonas putida. We thereby concentrated on quaternary ammonium salts. Analyzed compounds were composed of dicamba or MCPP moieties and cation with various alkyl chain lengths (n = 6,8,10) We compared them with commercial herbicides, and ammonium-based ionic liquids with neutral anion (Br^-). In addition, cis-trans isomerisation of unsaturated membrane fatty acids in Pseudomonas putida was applied as the proxy for toxicity and membrane activity. We showed that toxicity increased with the length of alkyl chains. However, this correlation is only valid for six and eight carbon atom in alkyl chains, where for n = 10 the EC₅₀ values rise by one order of magnitude. In our studies, the herbicidal ionic liquids [C₁₀,C₁₀,C₁,C₁N][MCPP] and [C₁₀,C₁₀,C₁,C₁N][dicamba] showed the lowest toxicity among analyzed quaternary ammonium salts and comparable toxicity with corresponding herbicides. No clear increase in toxicity could be followed by changing the anion moieties for ammonium-based ionic liquid forms.

Interference Competition Among Household Strains of Pseudomonas

Bacterial species exhibit biogeographical patterns like those observed in larger organisms. The distribution of bacterial species is driven by environmental selection through abiotic and biotic factors as well dispersal limitations. We asked whether interference competition, a biotic factor, could explain variability in habitat use by Pseudomonas species in the human home. To answer this question, we screened almost 8000 directional, pairwise interactions between 89 Pseudomonas strains including members of the Pseudomonas aeruginosa (n = 29), Pseudomonas fluorescens (n = 21), and Pseudomonas putida (n = 39) species groups for the presence of killing. This diverse set of Pseudomonas strains includes those isolated from several different habitats within the home environment and includes combinations of strains that were isolated from different spatial scales. The use of this strain set not only allowed us to analyze the commonality and phylogenetic scale of interference competition within the genus Pseudomonas but also allowed us to investigate the influence of spatial scale on this trait. Overall, the probability of killing was found to decrease with increasing phylogenetic distance, making it unlikely that interference competition accounts for previously observed differential habitat use among Pseudomonas species and species groups. Strikingly, conspecific P. aeruginosa killing accounted for the vast majority of the observed killing, and this killing was found to differ across the habitat type and spatial scale of the strains' isolation. These data suggest that interference competition likely plays a large role in the within-species dynamics of P. aeruginosa but not other household Pseudomonas species.

Comparative study of wastewater treatment and nutrient recycle via activated sludge, microalgae and combination systems

Algal-bacterial synergistic cultivation could be an optional wastewater treatment technology in temperate areas. In this study, a locally screened vigorous Chlorella strain was characterized and then it was used in a comparative study of wastewater treatment and nutrient recycle assessment via activated sludge (AS), microalgae and their combination systems. Chlorella sp. cultured with AS in light showed the best performance, in which case the removal efficiencies of COD, NH3-N and TP were 87.3%, 99.2% and 83.9%, respectively, within a short period of 1day. Algal-bacterial combination in light had the best settleability. Chlorella sp. contained biomass, could be processed to feed, fertilizer or fuel due to the improved quality (higher C/H/N) compared with sludge. PCR-DGGE analysis shows that two types of rhizobacteria, namely, Pseudomonas putida and Flavobacterium hauense were enriched in sludge when cultured with algae in light, serving as the basics for artificial consortium construction for improved wastewater treatment.

Numerical modelling of biophysicochemical effects on multispecies reactive transport in porous media involving Pseudomonas putida for potential microbial enhanced oil recovery application

pH and resident time of injected slug plays a critical role in characterizing the reservoir for potential microbial enhanced oil recovery (MEOR) application. To investigate MEOR processes, a multispecies (microbes-nutrients) reactive transport model in porous media was developed by coupling kinetic and transport model. The present work differs from earlier works by explicitly determining parametric values required for kinetic model by experimental investigations using Pseudomonas putida at different pH conditions and subsequently performing sensitivity analysis of pH, resident time and water saturation on concentrations of microbes, nutrients and biosurfactant within reservoir. The results suggest that nutrient utilization and biosurfactant production are found to be maximum at pH 8 and 7.5 respectively. It is also found that the sucrose and biosurfactant concentrations are highly sensitive to pH rather than reservoir microbial concentration, while at larger resident time and water saturation, the microbial and nutrient concentrations were lesser due to enhanced dispersion.

Metabolomics Analysis Reveals the Participation of Efflux Pumps and Ornithine in the Response of Pseudomonas putida DOT-T1E Cells to Challenge with Propranolol

Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden addition of 0.2, 0.4 and 0.6 mg mL^-1 of this β-blocker to several strains of P. putida, including the wild type DOT-T1E and the efflux pump knockout mutants DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the efflux pump TtgABC plays a more important role than the TtgGHI pump in strain tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a rapid, high-throughput screening tool to investigate any phenotypic changes resulting from exposure to varying levels of propranolol. Multivariate statistical analysis of these MIR data revealed gradient trends in resultant ordination scores plots, which were related to the concentration of propranolol. MIR illustrated phenotypic changes associated with the presence of this drug within the cell that could be assigned to significant changes that occurred within the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during the growth of bacteria following toxic perturbation with the same concentration levels of propranolol. Metabolic profiling revealed that ornithine, which was only produced by P. putida cells in the presence of propranolol, presents itself as a major metabolic feature that has important functions in propranolol stress tolerance mechanisms within this highly significant and environmentally relevant species of bacteria.

Regulation of Hydroxylation and Nitroreduction Pathways during Metabolism of the Neonicotinoid Insecticide Imidacloprid by Pseudomonas putida

Imidacloprid (IMI) is mainly metabolized via nitroreduction and hydroxylation pathways, which produce different metabolites that are toxic to mammals and insects. However, regulation of IMI metabolic flux between nitroreduction and hydroxylation pathways is still unclear. In this study, Pseudomonas putida was found to metabolize IMI to 5-hydroxy and nitroso IMI and was therefore used for investigating the regulation of IMI metabolic flux. The cell growth time, cosubstrate, dissolved oxygen concentration, and pH showed significant effect on IMI degradation and nitroso and 5-hydroxy IMI formation. Gene cloning and overexpression in Escherichia coli proved that P. putida KT2440 aldehyde oxidase mediated IMI nitroreduction to nitroso IMI, while cytochrome P450 monooxygenase (CYP) failed to improve IMI hydroxylation. Moreover, E. coli cells without CYP could hydroxylate IMI, demonstrating the role of a non-CYP enzyme in IMI hydroxylation. Thus, the present study helps to further understand the environmental fate of IMI and its underlying mechanism.

Toxicity of graphene oxide on growth and metabolism of Pseudomonas putida

The increasing consumption of graphene derivatives leads to greater presence of these materials in wastewater treatment plants and ecological systems. The toxicity effect of graphene oxide (GO) on the microbial functions involved in the biological wastewater treatment process is studied, using Pseudomonas putida and salicylic acid (SA) as bacterial and pollutant models. A multiparametric flow cytometry (FC) method has been developed to measure the metabolic activity and viability of P. putida in contact with GO. A continuous reduction in the percentages of viable cells and a slight increase, lower than 5%, in the percentages of damaged and dead cells, suggest that P. putida in contact with GO loses the membrane integrity but preserves metabolic activity. The growth of P. putida was strongly inhibited by GO, since 0.05mgmL(-1) of GO reduced the maximum growth by a third, and the inhibition was considerably greater for GO concentrations higher than 0.1mgmL(-1). The specific SA removal rate decreased with GO concentration up to 0.1mgmL(-1) indicating that while GO always reduces the growth of P. putida, for concentrations higher than 0.1mgmL(-1), it also reduces its activity. Similar behaviour is observed using simulated urban and industrial wastewaters, the observed effects being more acute in the industrial wastewaters.

In situ non-destructive measurement of biofilm thickness and topology in an interferometric optical microscope

Biofilms are ubiquitous and impact the environment, human health, dental hygiene, and a wide range of industrial processes. Biofilms are difficult to characterize when fully hydrated, especially in a non-destructive manner, because of their soft structure and water-like bulk properties. Herein a method of measuring and monitoring the thickness and topology of live biofilms of using white light interferometry is described. Using this technique, surface morphology, surface roughness, and biofilm thickness were measured over time without while the biofilm continued to grow. The thickness and surface topology of a P. putida biofilm were monitored growing from initial colonization to a mature biofilm. Measured thickness followed expected trends for bacterial growth. Surface roughness also increased over time and was a leading indicator of biofilm growth.

Impact of nanoscale zero valent iron on bacteria is growth phase dependent

The toxic effect of nanoscale zero valent iron (nZVI) particles on bacteria from different growth phases was studied. Four bacterial strains namely Escherichia coli strains JM109 and BW25113, and Pseudomonas putida strains KT2440 and F1 were experimented. The growth curves of these strains were determined. Bacterial cells were harvested based on the predetermined time points, and exposed to nZVI. Cell viability was determined by the plate count method. Bacterial cells in lag and stationary phases showed higher resistance to nZVI for all four bacterial strains, whereas cells in exponential and decline phases were less resistant to nZVI and were rapidly inactivated when exposed to nZVI. Bacterial inactivation increased with the concentration of nZVI. Furthermore, less than 14% bacterial inactivation was observed when bacterial cells were exposed to the filtrate of nZVI suspension suggesting that the physical interaction between nZVI and cell is necessary for bacterial inactivation.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

Graphical abstract

Sustainable production of valuable compound 3-succinoyl-pyridine by genetically engineering Pseudomonas putida using the tobacco waste

Treatment of solid and liquid tobacco wastes with high nicotine content remains a longstanding challenge. Here, we explored an environmentally friendly approach to replace tobacco waste disposal with resource recovery by genetically engineering Pseudomonas putida. The biosynthesis of 3-succinoyl-pyridine (SP), a precursor in the production of hypotensive agents, from the tobacco waste was developed using whole cells of the engineered Pseudomonas strain, S16dspm. Under optimal conditions in fed-batch biotransformation, the final concentrations of product SP reached 9.8 g/L and 8.9 g/L from aqueous nicotine solution and crude suspension of the tobacco waste, respectively. In addition, the crystal compound SP produced from aqueous nicotine of the tobacco waste in batch biotransformation was of high purity and its isolation yield on nicotine was 54.2%. This study shows a promising route for processing environmental wastes as raw materials in order to produce valuable compounds.

Detecting total toxicity in water using a mediated biosensor system with flow injection

A novel total toxicity detection method based on a mediated biosensor system with flow injection (MB-FI) was developed to rapidly and reliably detect respiration inhibitors (i.e., As2O3, KCN, salicylic acid (SA), 2,4-dintirophenol (DNP)) in water. The mediated biosensor toxicity assessment using microorganisms immobilized in calcium alginate filaments can greatly simplify the testing process and save time. In the MB-FI system, ferricyanide together with a respiration inhibitor was injected into the bioreactor, inhibiting the respiration of the immobilized microorganisms. The degree of inhibition was measured by determining the ferrocyanide generated in the effluent, expressed as the 50% inhibition concentration (IC50). The IC50 values for the four respiration inhibitors obtained using this method were comparable to those obtained using the classic method, confirming that this approach is an alternative alert method. More importantly, this constructed biosensor system with flow injection will facilitate the application and commercialization of this toxicity monitoring technology.

Assessment of toxicity and biodegradability on activated sludge of priority and emerging pollutants

Several methods for evaluating the toxicity and biodegradability of hazardous pollutants (chlorinated compounds, chemical additives and pharmaceuticals) have been studied in this work. Different bioassays using representative bacteria of marine and terrestrial ecosystems such as Vibrio fischeri and Pseudomonas putida have been used to assess the ecotoxicity. Activated sludge was used to analyse the effect of those pollutants in a biological reactor of a sewage treatment plant (STP). The results demonstrate that none of the compounds is toxic to activated sludge, except ofloxacin to P. putida. The additives tested can be considered moderately toxic according to the more sensitive V. fischeri assays, whereas the EC50 values of the pharmaceuticals depend on the specific microorganism used in each test. Regarding the biodegradability, respirometric measurements were carried out for fast biodegradability assessment and the Zahn-Wellens test for inherent biodegradability. The evolution of the specific oxygen uptake rate (SOUR) showed that only diethyl phthalate was easily biodegradable and acetylsalicylic acid was partially biodegradable (98% and 65% degradation, respectively). The persistence of dichloromethane, ofloxacin and hidrochlorothiazide was confirmed along the 28 days of the Zahn-Wellens test whereas 1,1,1-trichloroethane showed inherent biodegradability (74% removal). Most of the chlorinated compounds, pharmaceuticals, bisphenol A and ethylenediaminetetraacetic acid were partially degraded in 28 d with total organic carbon (TOC) reduction ranging from 21% to 51%. Sulphamethoxazole showed certain biodegradation (50% removal) with TOC decrease around 31%, which indicates the formation of non-biodegradable by-products.

Non-Selective Evolution of Growing Populations

Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997). Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck). We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions “freezes” to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009) as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923) for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift), which investigated how traits spread and eventually take over populations (fixate) (Kimura, 1955; Otto and Whitlock, 1997). Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012) of periodically shrinking and expanding populations.

Cometabolism of methyl tert-butyl ether by a new microbial consortium ERS

The release of methyl tert-butyl-ether (MTBE) into the environment has increased the worldwide concern about the pollution of MTBE. In this paper, a microbial consortium was isolated from the soil sample near an oil station, which can degrade MTBE directly with a low biomass yield and MTBE degrading efficiency. Further research has indicated that this consortium can degrade MTBE efficiently when grown on n-octane as the cometabolic substrate. The results of 16S rDNA based on phylogenetic analysis of the selected operating taxonomic units (OTUs) involved in the consortium revealed that one OTU was related to Pseudomonas putida GPo1, which could cometabolically degrade MTBE on the growth of n-octane. This may help explain why n-octane could be the optimal cometabolic substrate of the consortium for MTBE degradation. Furthermore, the degradation of MTBE was observed along with the consumption of n-octane. Different K s values for MTBE were observed for cells grown with or without n-octane, suggesting that different enzymes are responsible for the oxidation of MTBE in cells grown on n-octane or MTBE. The results are discussed in terms of their impacts on our understanding of MTBE biodegradation and cometabolism.

Dynamics of suspended and attached aerobic toluene degraders in small-scale flow-through sediment systems under growth and starvation conditions

The microbially mediated reactions, that are responsible for field-scale natural attenuation of organic pollutants, are governed by the concurrent presence of a degrading microbial community, suitable energy and carbon sources, electron acceptors, as well as nutrients. The temporal lack of one of these essential components for microbial activity, arising from transient environmental conditions, might potentially impair in situ biodegradation. This study presents results of small scale flow-through experiments aimed at ascertaining the effects of substrate-starvation periods on the aerobic degradation of toluene by Pseudomonas putida F1. During the course of the experiments, concentrations of attached and mobile bacteria, as well as toluene and oxygen were monitored. Results from a fitted reactive-transport model, along with the observed profiles, show the ability of attached cells to survive substrate-starvation periods of up to four months and suggest a highly dynamic exchange between attached and mobile cells under growth conditions and negligible cell detachment under substrate-starvation conditions. Upon reinstatement of toluene, it was readily degraded without a significant lag period, even after a starvation period of 130 days. Our experimental and modeling results strongly suggest that aerobic biodegradation of BTEX-hydrocarbons at contaminated field sites is not hampered by intermittent starvation periods of up to four months.

Effect of silver nanoparticles on Pseudomonas putida biofilms at different stages of maturity

This study determined the effect of silver nanoparticles (AgNPs) on Pseudomonas putida KT2440 biofilms at different stages of maturity. Three biofilm stages (1-3, representing early to late stages of development) were identified from bacterial adenosine triphosphate (ATP) activity under static (96-well plate) and dynamic conditions (Center for Disease Control and Prevention biofilm reactor). Extracellular polymeric substance (EPS) levels, measured using crystal violet and total carbohydrate assays, and expression of the EPS-associated genes, csgA and alg8, supported the conclusion that biofilms at later stages were older than those at earlier stages. More mature biofilms (stages 2 and 3) showed little to no reduction in ATP activity following exposure to AgNPs. In contrast, the same treatment reduced ATP activity by more than 90% in the less mature stage 1 biofilms. Regardless of maturity, biofilms with EPS stripped off were more susceptible to AgNPs than controls with intact EPS, demonstrating that EPS is critical for biofilm tolerance of AgNPs. The findings from this study show that stage of maturity is an important factor to consider when studying effect of AgNPs on biofilms.

[The role of mineral phosphorus compounds in naphthalene biodegradation by Pseudomonas putida]

The effect of phosphate concentration in the culture medium on the growth and naphthalene degradation by Pseudomonas putida BS 3701 was studied. The limiting concentration of phosphate was 0.4 mM and 0.1 mM under cultivation in media with naphthalene and glucose, respectively The phosphate deficiency correlated with a decrease in the activities of naphthalene dioxygenase and salicylate hydroxylase and with salicylate accumulation in the culture medium. We suggest that this fact indicates the impaired regulation of gene expression of "upper" and "lower" pathways of naphthalene oxidation. Under naphthalene degradation, the cells accumulated three times more inorganic polyphosphates as compared with the consumption of glucose. The involvement of polyphosphates in the regulation of naphthalene metabolism has been considered.

Hormetic effect of ionic liquid 1-ethyl-3-methylimidazolium acetate on bacteria

The biological effect of ionic liquids (ILs) is one of the highly debated topics as they are being contemplated for various industrial applications. 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) showed remarkable hormesis on anaerobic Clostridium sp. and aerobic Pseudomonas putida. Bacterial growth was stimulated at up to 2.5 g L(-1) and inhibited at >2.5 g L(-1) of [EMIM][Ac]. The growth of Clostridium sp. and P. putida were higher by 0.4 and 4-fold respectively, in the presence of 0.5 g L(-1) [EMIM][Ac]. Assessment of the effect of [EMIM][Ac] under different growth conditions showed that the hormesis of [EMIM][Ac] was mediated via regulation of medium pH. Hormetic effect of [EMIM][Ac] was evident only in medium with poor buffering capacity and in the presence of a fermentable substrate as the carbon source. The hormetic effect of [EMIM][Ac] on bacterial growth is most likely associated with the buffering capacity of acetate anion. These observations have implications in ILs toxicity studies and ecological risk assessment.

A comparison of the sorption reactivity of bacteriogenic and mycogenic Mn oxide nanoparticles

Biogenic MnO2 minerals affect metal fate and transport in natural and engineered systems by strongly sorbing metals ions. The ability to produce MnO2 is widely dispersed in the microbial tree of life, leading to potential differences in the minerals produced by different organisms. In this study, we compare the structure and reactivity of biogenic Mn oxides produced by the biofilm-forming bacterium Pseudomonas putida GB-1 and the white-rot fungus Coprinellus sp. The rate of Mn(II) oxidation, and thus biomineral production, was 45 times lower for Coprinellus sp. (5.1 × 10(-2) mM d(-1)) than for P. putida (2.32 mM d(-1)). Both organisms produced predominantly Mn(IV) oxides with hexagonal-sheet symmetry, low sheet stacking, small particle size, and Mn(II/III) in the interlayer. However, we found that mycogenic MnO2 could support a significantly lower quantity of Ni sorbed via inner-sphere coordination at vacancy sites than the bacteriogenic MnO2: 0.09 versus 0.14 mol Ni mol(-1) Mn. In addition, 50-100% of the adsorbed Ni partitioned to the MnO2, which accounts for less than 20% of the sorbent on a mass basis. The vacancy content, which appears to increase with the kinetics of MnO2 precipitation, exerts significant control on biomineral reactivity.

Effect of heavy-metal-resistant bacteria on enhanced metal uptake and translocation of the Cu-tolerant plant, Elsholtzia splendens

A hydroponics trial was employed to study the effects of Pseudomonas putida CZ1 (CZ1), a heavy-metal-resistant bacterial strain isolated from the rhizosphere of Elsholtzia splendens (E. splendens), on the uptake and translocation of copper (Cu) in E. splendens. Significant promotion of plant growth coupled with the obvious plant-growth-promoting (PGP) characters of the bacteria suggested that CZ1 would be a plant-growth-promoting rhizobacterium (PGPR) to E. splendens under Cu stress condition. The results of inductively coupled plasma optical emission spectrometry (ICP-OES) showed that CZ1 increased the concentration of Cu in the shoots (up to 211.6% compared to non-inoculation treatment) and translocation factor (TF) (from 0.56 to 1.83%) of those exposed to Cu. The distribution of Cu in root cross section measured by synchrotron-based X-ray fluorescence microscopy (SRXRF) indicated that CZ1 promoted the transport of Cu from cortex to xylem in roots, which contributed to the accumulation of Cu in shoots. Furthermore, CZ1 improved the uptake of nutrient elements by plants to oppose to the toxicity of Cu. In summary, P. putida CZ1 acted as a PGPR in resistance to Cu and promoted the accumulation and translocation of Cu from root to shoot by element redistribution in plant root; hence, CZ1 is a promising assistance to phytoremediation.

The c-di-GMP phosphodiesterase BifA regulates biofilm development in Pseudomonas putida

We previously showed the isolation of biofilmpersistent Pseudomonas putida mutants that fail to undergo biofilm dispersal upon entry in stationary phase. Two such mutants were found to bear insertions in PP0914, encoding a GGDEF/EAL domain protein with high similarity to Pseudomon asaeruginosa BifA. Here we show the phenotypic characterization of a ΔbifA mutant in P. putida KT2442.This mutant displayed increased biofilm and pellicle formation, cell aggregation in liquid medium and decreased starvation-induced biofilm dispersal relative to the wild type. Unlike its P. aeruginosa counterpart, P. putida BifA did not affect swarming motility. The hyperadherent phenotype of the ΔbifA mutant correlates with a general increase in cyclic diguanylate (c-di-GMP) levels, Congo Red-binding exopolyaccharide production and transcription of the adhesin-encoding lapA gene. Integrity of the EAL motif and a modified GGDEF motif (altered to GGDQF)were crucial for BifA activity, and c-di-GMP depletion by overexpression of a heterologous c-di-GMP phosphodiesterase in the ΔbifA mutant restored wild-type biofilm dispersal and lapA expression.Our results indicate that BifA is a phosphodiesterase involved in the regulation of the c-di-GMP pool and required for the generation of the low c-di-GMP signal that triggers starvation-induced biofilm dispersal.

Experimental and kinetic study on the cometabolic biodegradation of phenol and 4-chlorophenol by psychrotrophic Pseudomonas putida LY1

This study investigated the kinetics of phenol and 4-chlorophenol (4-CP) biodegradation by a cold-adapted bacteria, Pseudomonas putida LY1, isolated from Songhua River sediment. The results showed that P. putida LY1 cannot grow on 4-CP as a sole carbon source. P. putida LY1 had the potential to cometabolic biodegrade phenol and 4-CP in a wide range of temperature (varying from 5 to 35 °C) with the optimal temperature around 25 °C. Mixture of phenol and 4-CP were completely removed at two 4-CP concentrations (15 and 40 mg/L) over a wide range of phenol (20-400 mg/L) concentrations, whereby the ratio of 4-CP/biomass (S 2/X) was lower than 0.03. The kinetic models of cometabolic biodegradation of phenol and 4-CP were proposed, considering the growth and nongrowth substrate inhibition. These models successfully simulate the processes of cometabolic degradation of phenol and 4-CP.