SummarySynthetic plastics, which are widely present in materials of everyday use, are ubiquitous and slowly-degrading polymers in environmental wastes. Of special interest are the capabilities of microorganisms to accelerate their degradation. Members of the metabolically diverse genus Pseudomonas are of particular interest due to their capabilities to degrade and metabolize synthetic plastics. Pseudomonas species isolated from environmental matrices have been identified to degrade polyethylene, polypropylene, polyvinyl chloride, polystyrene, polyurethane, polyethylene terephthalate, polyethylene succinate, polyethylene glycol and polyvinyl alcohol at varying degrees of efficiency. Here, we present a review of the current knowledge on the factors that control the ability of Pseudomonas sp. to process these different plastic polymers and their by-products. These factors include cell surface attachment within biofilms, catalytic enzymes involved in oxidation or hydrolysis of the plastic polymer, metabolic pathways responsible for uptake and assimilation of plastic fragments and chemical factors that are advantageous or inhibitory to the biodegradation process. We also highlight future research directions required in order to harness fully the capabilities of Pseudomonas sp. in bioremediation strategies towards eliminating plastic wastes.

A simplified overflow model (depicted as a rain barrel) is proposed to explain how ethanol is produced during syngas fermentation.

A recent study of the effect of pH on Zn and Cd bioavailability shows that binding to weak organic ligands can increase the pool of metals available to phytoplankton in the presence of strong chelating agents. We explore the underlying mechanism in laboratory experiments with the model species Emiliania huxleyi and Thalassiosira weissflogii. Additions of L- and D- isomers of cysteine (Cys) result in similar increases in Zn uptake rates in the presence of the strong chelator ethylenediaminetetraacetic acid (EDTA) but decrease it in the absence of EDTA, ruling out uptake by a specific Zn-Cys transporter. The effect of Cys does not result from alleviating diffusion limitation of inorganic Zn. The enhancement of Zn uptake kinetics by weak ligands is consistent with a mechanism involving formation of a transient ternary complex with uptake molecules: (1) the enhancement is most dramatic in Zn limited cells whose high affinity transporters should be most effective at extracting Zn from weak ligands; (2) the enhancement occurs with a variety of weak ligands, demonstrating that the underlying mechanism has little chemical specificity; and (3) no enhancement of uptake is seen when Zn is bound in complexes that would make formation of multiligand complexes with uptake molecules difficult. Weak complexing agents which have received heretofore little attention may play a key role in the bioavailability of metals in natural waters.

Binding of antibiotics to clay minerals can decrease both their physical and biological availability in soils. To elucidate the binding mechanisms of tetracycline antibiotics on smectite clays as a function of pH, we probed the interactions of oxytetracycline (OTC) with Na-montmorillonite (MONT) using X-ray diffraction (XRD), infrared (IR), and solid-state nuclear magnetic resonance (NMR) spectroscopies, and Monte Carlo molecular simulations. The XRD patterns demonstrate the presence of OTC in the MONT interlayer space at acidic pH whereas complexation of OTC by external basal and edge sites seems to prevail at pH 8. At both pH, the (1)H-(13)C NMR profile indicates restricted mobility of the adsorbed OTC species; and, -CH(3) deformation and C-N stretching IR vibration bands confirm a binding mechanism involving the protonated dimethylamino group of OTC. Changes in the (23)Na NMR environments are consistent with cation-exchange and cation complexation reactions at the different sites of adsorption. Molecular simulations indicate that MONT interlayer spacing and structural charge localization dictate favorable binding conformations of the intercalated OTC, facilitating multiple interactions in agreement with the spectroscopic data. Our results present complementary insights into the mechanisms of adsorption of TETs on smectites important for their retention in natural and engineered soil environments.

Decreased biomass growth in iron (Fe)‐limited Pseudomonas is generally attributed to downregulated expression of Fe‐requiring proteins accompanied by an increase in siderophore biosynthesis. Here, we applied a stable isotope‐assisted metabolomics approach to explore the underlying carbon metabolism in glucose‐grown Pseudomonas putida KT2440. Compared to Fe‐replete cells, Fe‐limited cells exhibited a sixfold reduction in growth rate but the glucose uptake rate was only halved, implying an imbalance between glucose uptake and biomass growth. This imbalance could not be explained by carbon loss via siderophore production, which accounted for only 10% of the carbon‐equivalent glucose uptake. In lieu of the classic glycolytic pathway, the Entner–Doudoroff (ED) pathway in Pseudomonas is the principal route for glucose catabolism following glucose oxidation to gluconate. Remarkably, gluconate secretion represented 44% of the glucose uptake in Fe‐limited cells but only 2% in Fe‐replete cells. Metabolic 13C flux analysis and intracellular metabolite levels under Fe limitation indicated a decrease in carbon fluxes through the ED pathway and through Fe‐containing metabolic enzymes. The secreted siderophore was found to promote dissolution of Fe‐bearing minerals to a greater extent than the high extracellular gluconate. In sum, bypasses in the Fe‐limited glucose metabolism were achieved to promote Fe availability via siderophore secretion and to reroute excess carbon influx via enhanced gluconate secretion.

Pseudomonas species thrive in different nutritional environments and can catabolize divergent carbon substrates. These capabilities have important implications for the role of these species in natural and engineered carbon processing. However, the metabolic phenotypes enabling Pseudomonas to utilize mixed substrates remain poorly understood. Here, we employed a multi-omics approach involving stable isotope tracers, metabolomics, fluxomics, and proteomics in Pseudomonas putida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucose and benzoate, respectively a monomer of carbohydrate polymers and a derivative of lignin monomers. Despite nearly equal consumption of both substrates, metabolite isotopologues revealed nonuniform assimilation throughout the metabolic network. Gluconeogenic flux of benzoate-derived carbons from the tricarboxylic acid cycle did not reach the upper Embden-Meyerhof-Parnas pathway nor the pentose-phosphate pathway. These latter two pathways were populated exclusively by glucose-derived carbons through a cyclic connection with the Entner-Doudoroff pathway. We integrated the 13 C-metabolomics data with physiological parameters for quantitative flux analysis, demonstrating that the metabolic segregation of the substrate carbons optimally sustained biosynthetic flux demands and redox balance. Changes in protein abundance partially predicted the metabolic flux changes in cells grown on the glucose:benzoate mixture versus on glucose alone. Notably, flux magnitude and directionality were also maintained by metabolite levels and regulation of phosphorylation of key metabolic enzymes. These findings provide new insights into the metabolic architecture that affords adaptability of P. putida to divergent carbon substrates and highlight regulatory points at different metabolic nodes that may underlie the high nutritional flexibility of Pseudomonas species. This work was supported by an Integrative Graduate Education and Research Traineeship Fellowship from the National Science Foundation (to M. A. K.), graduate fellowships from Cornell University (to M. S. and R. A. W.), and a start-up package from Cornell University. The authors declare that they have no conflicts of interest with the contents of this article. This article contains Tables S1-S4 and Figs. S1-S6.

In natural samples from the New Jersey coast and the Gulf of Alaska, zinc (Zn) and cadmium (Cd) uptake rates by phytoplankton decreased on average about 30% as pH was decreased from 8.5 to 7.9 or 7.7, and the partial pressure of carbon dioxide (PCO2) increased accordingly. The underlying mechanism was explored with the model species, Thalassiosira weissflogii and Emiliania huxleyi, using ethylenediaminetetraacetic acid (EDTA), desferrioxamine B, phytochelatin, and cysteine as complexing agents. Experiments with single complexing agents did not reproduce the effect of pH seen in field samples, ruling out two possible mechanisms: a direct effect on the uptake machinery or down‐regulation of uptake at high PCO2. Zn and Cd bioavailability must thus somehow decrease at low pH in natural seawater, which is counterintuitive since the protonation of complexing agents at low pH should increase the total free concentration of metals. However, in the presence of both a strong and a weak complexing agent, metal uptake rate may decrease at low pH if formation of the weak complex decreases and the metal in the weak complex is more “available” than in the strong complex. We obtained proof of concept for such a two‐ligand mechanism for Zn uptake in the presence of EDTA + phytochelatin and EDTA + cysteine. Weak ligands that bind a small fraction of essential metals in surface seawater may thus be important in metal uptake by phytoplankton, and the dual effects of strong and weak complexing agents may control not just the magnitude but also the sign of the effect of pH‐PCO2 on metal uptake rates.

Previous studies have reported adverse effects of glyphosate on crop-beneficial soil bacterial species, including several soil Pseudomonas species. Of particular interest is the elucidation of the metabolic consequences of glyphosate toxicity in these species. Here we investigated the growth and metabolic responses of soil Pseudomonas species grown on succinate, a common root exudate, and glyphosate at different concentrations. We conducted our experiments with one agricultural soil isolate, P. fluorescens RA12, and three model species, P. putida KT2440, P. putida S12, and P. protegens Pf-5. Our results demonstrated both species-and strain-dependent growth responses to glyphosate. Following exposure to a range of glyphosate concentrations (up to 5 mM), the growth rate of both P. protegens Pf-5 and P. fluorescens RA12 remained unchanged whereas the two P. putida strains exhibited from 0 to 100% growth inhibition. We employed a 13 C-assisted metabolomics approach using liquid chromatography-mass spectrometry to monitor disruptions in metabolic homeostasis and fluxes. Profiling of the whole-cell metabolome captured deviations in metabolite levels involved in the tricarboxylic acid cycle, ribonucleotide biosynthesis, and protein biosynthesis. Altered metabolite levels specifically in the biosynthetic pathway of aromatic amino acids (AAs), the target of toxicity for glyphosate in plants, implied the same toxicity target in the soil bacterium. Kinetic flux experiments with 13 C-labeled succinate revealed that biosynthetic fluxes of the aromatic AAs were not inhibited in P. fluorescens Pf-5 in the presence of low and high glyphosate doses but these fluxes were inhibited by up to 60% in P. putida KT2440, even at sub-lethal glyphosate exposure. Notably, the greatest inhibition was found for the aromatic AA tryptophan, an important precursor to secondary metabolites. When the growth medium was supplemented with aromatic AAs, P. putida S12 exposed to a lethal dose of glyphosate completely recovered in terms of both growth rate and selected Aristilde et al.Metabolomics of Glyphosate Effects on Soil Bacteria metabolite levels. Collectively, our findings led us to conclude that the glyphosateinduced specific disruption of de novo biosynthesis of aromatic AAs accompanied by widespread metabolic disruptions was responsible for dose-dependent adverse effects of glyphosate on sensitive soil Pseudomonas species.