Characterization of proton production and consumption associated with microbial metabolism

Novel method of removing metals from estuarine water using whole microbial mats

This study addresses the limited understanding of chromium-microbial mat interactions in estuarine tidal flats. The aims were to evaluate (1) the efficiency of the microbial consortium in Cr(III) removal from seawater; (2) the elemental and mineralogical composition of the microbial mat as a natural system in the Cr removal, (3) the effects of metal on microphytobenthos, and (4) possible interactions of Cr with other metals present in the consortium. Microbial mats were exposed to Cr(III) solutions at different concentrations (2-30 mg Cr/L). Analysis such as metal concentration, organic matter content, chlorophyll a and phaeopigment concentrations, abundance of diatoms and cyanobacteria, SEM-EDS, and XRD were performed. Most of the Cr(III) was deposited, as chromium oxide/hydroxide, on the surface of all microbial mat components. The complete microbial mat, comprising sediments, detritus, EPS, and diverse microorganism communities, exhibited a remarkable capacity to accumulate Cr(III), retaining over 87% in the solution.

Biodegradable and pH-Responsive Amphiphilic Poly(succinimide) Derivatives for Triggered Release of Antibiotics for Management of Infected Wounds

Wound infection has become a healthy economic burden globally. Current wound management mainly relies on the use of antibiotics; however, the misuse and overuse of antibiotics can easily result in antibiotic resistance. This study proposes a biodegradable, biocompatible, and pH-responsive amphiphilic 11-aminoundecanoic acid-grafted polysuccinimide (AUA-PSI) as a nanocarrier for drug encapsulation via nanoprecipitation. The succinimide groups in the backbone of PSI allow facile postfunctionalization via an aminolysis reaction. The degree of substitution of AUA can be modulated to adjust the degradation rate, pH sensitivity, and drug-release profile. Antibiotic rifampicin was incorporated with AUA-PSI to form Rif-AUA-PSI nanoparticles and demonstrated pH-responsiveness and antimicrobial activity. Because of the elevation of the pH value from pH = ∼ 5.5 in healthy skin to pH > 7 in an infected wound, Rif-AUA-PSI nanoparticles begin to decompose and release Rif upon the hydrolysis of succinimide/amide and deprotonation of carboxyl groups. The effective suppression of bacterial growth by Rif-AUA-PSI nanoparticles was demonstrated using a plate count method. More importantly, Rif-AUA-PSI nanoparticles were physically deposited on cotton gauze bandages as an antibiotic wound dressing. The Rif-AUA-PSI-modified gauze was applied to infected wounds on rats for wound management. The results show fast wound healing and inhibition of bacterial growth, which demonstrate that the method promotes modulable amphiphilicity, biodegradability, biocompatibility, pH-responsiveness, and facile modification for nanomedicine and medical devices.

Enhancement of phytoextraction efficiency coupling Pteris vittata with low-dose biochar in arsenic-contaminated soil

Phytoremediation of arsenic (As) by Pteris vittata (P. vittata) is a cost-effective and environmentally friendly method for restoring As-contaminated sites. However, the phytoextraction efficiency is low in some cases, such as clay soil, thus biochar was applied to enhance the efficiency of As extraction. The paper investigated the effect of biochar on soil characteristic, As mobility, and As uptake in P. vittata with a 90-day greenhouse experiment. Biochar derived from rice straw was added at rates of 0.5, 1.5, and 4% (w/w). The results showed that, under biochar amendment, soil pH raised from 5.24 to 6.03 and 4.91 to 5.85, soil dissolved organic carbon (DOC) increased 11.1-46.1% and 2.8-11.2%, respectively, in rhizosphere and bulk soils. Biochar also increased soil catalase (CAT) activity significantly, especially for the rhizosphere soil. Besides, biochar increased the labile As in the soils and transfer coefficient from roots to aboveground, thereby enhancing As accumulation by P. vittata tissues. The accumulation of As in fronds of P. vittata was up to 350 mg kg-1 in 1.5% biochar, which was more than twice the control and far beyond other biochar treatments. The results indicate that biochar addition is favorable to improve phytoremediation of P. vittata in As-contaminated soil and 1.5% (w/w) biochar may be a reasonable application ratio, thus providing an effective solution to enhance the efficiency of As phytoextraction.

Fabrication of a Vitamin B12-Loaded Carbon Dot/Mixed-Ligand Metal Organic Framework Encapsulated within the Gelatin Microsphere for pH Sensing and In Vitro Wound Healing Assessment

Bacterial invasion is a serious concern during the wound healing process. The colonization of bacteria is mainly responsible for the pH fluctuation at the wound site. Therefore, the fabrication of a proper wound dressing material with antibacterial activity and pH monitoring ability is necessary to acquire a fast healing process. Therefore, this work is dedicated to designing a vitamin B12-loaded gelatin microsphere (MS) decorated with a carbon dot (CD) metal-organic framework (MOF) for simultaneous pH sensing and advanced wound closure application. The resultant MS portrayed a high specific surface area and a hierarchically porous structure. Furthermore, the surface of the resultant MS contained numerous carboxyl groups and amine groups whose deprotonation and protonation with the pH alternation are accountable for the pH-sensitive properties. The vitamin B12 release study was speedy from the MOF structure in an acidic medium, which was checked by gelatin coating, and a controlled drug release behavior was observed. The system showed excellent cytocompatibility toward the L929 cell line and remarkable antibacterial performance against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Furthermore, the combined effect of Zn²⁺, the imidazole unit, and CDs produces an outstanding bactericidal effect on the injury sites. Finally, the in vitro wound model suggests that the presence of the vitamin B12-loaded gelatin MS accelerates the proliferation of resident fibroblast L929 cells and causes tissue regeneration in a time-dependent manner. The relative wound area, % of wound closure, and wound healing speed values are remarkable and suggest the requirement for assessing the response of the system before exploiting its prospective in vivo application.

Exploiting the role of nanoparticles for use in hydrogel-based bioprinting applications: concept, design, and recent advances

Three-dimensional (3D) bioprinting is an emerging tissue engineering approach that aims to develop cell or biomolecule-laden, complex polymeric scaffolds with high precision, using hydrogel-based "bioinks". Hydrogels are water-swollen, highly crosslinked polymer networks that are soft, quasi-solid, and can support and protect biological materials. However, traditional hydrogels have weak mechanical properties and cannot retain complex structures. They must be reinforced with physical and chemical manipulations to produce a mechanically resilient bioink. Over the past few years, we have witnessed an increased use of nanoparticles and biological moiety-functionalized nanoparticles to fabricate new bioinks. Nanoparticles of varied size, shape, and surface chemistries can provide a unique solution to this problem primarily because of three reasons: (a) nanoparticles can mechanically reinforce hydrogels through physical and chemical interactions. This can favorably influence the bioink's 3D printability and structural integrity by modulating its rheological, biomechanical, and biochemical properties, allowing greater flexibility to print a wide range of structures; (b) nanoparticles can introduce new bio-functionalities to the hydrogels, which is a key metric of a bioink's performance, influencing both cell-material and cell-cell interactions within the hydrogel; (c) nanoparticles can impart "smart" features to the bioink, making the tissue constructs responsive to external stimuli. Responsiveness of the hydrogel to magnetic field, electric field, pH changes, and near-infrared light can be made possible by the incorporation of nanoparticles. Additionally, bioink polymeric networks with nanoparticles can undergo advanced chemical crosslinking, allowing greater flexibility to print structures with varied biomechanical properties. Taken together, the unique properties of various nanoparticles can help bioprint intricate constructs, bringing the process one step closer to complex tissue structure and organ printing. In this review, we explore the design principles and multifunctional properties of various nanomaterials and nanocomposite hydrogels for potential, primarily extrusion-based bioprinting applications. We illustrate the significance of biocompatibility of the designed nanocomposite hydrogel-based bioink for clinical translation and discuss the different parameters that affect cell fate after cell-nanomaterial interaction. Finally, we critically assess the current challenges of nanoengineering bioinks and provide insight into the future directions of potential hydrogel bioinks in the rapidly evolving field of bioprinting.

Exploitation of ammonia-inducible promoters for enzyme overexpression in Bacillus licheniformis

Ammonium hydroxide is conventionally used as an alkaline reagent and cost-effective nitrogen source in enzyme manufacturing processes. However, few ammonia-inducible enzyme expression systems have been described thus far. In this study, genomic-wide transcriptional changes in Bacillus licheniformis CBBD302 cultivated in media supplemented with ammonia were analyzed, resulting in identification of 1443 differently expressed genes, of which 859 genes were upregulated and 584 downregulated. Subsequently, the nucleotide sequences of ammonia-inducible promoters were analyzed and their functionally-mediated expression of amyL, encoding an α-amylase, was shown. TRNA_RS39005 (copA), TRNA_RS41250 (sacA), TRNA_RS23130 (pdpX), TRNA_RS42535 (ald), TRNA_RS31535 (plp), and TRNA_RS23240 (dfp) were selected out of the 859 upregulated genes and each showed higher transcription levels (FPKM values) in the presence of ammonia and glucose than that of the control. The promoters, P_copA from copA, P_sacA from sacA, P_pdpX from pdpX, P_ald from ald, and P_plp from plp, except P_dfp from dfp, were able to mediate amyL expression and were significantly induced by ammonia. The highest enzyme expression level was mediated by P_plp and represented 23% more α-amylase activity after induction by ammonia in a 5-L fermenter. In conclusion, B. licheniformis possesses glucose-independent ammonia-inducible promoters, which can be used to mediate enzyme expression and therefore enhance the enzyme yield in fermentations conventionally fed with ammonia for pH adjustment and nitrogen supply.

Synthesis of a novel nanocomposite containing chitosan as a three-dimensional printed wound dressing technique: Emphasis on gene expression

In this study, a highly porous three-dimensional (3D)-printed wound healing core/shell scaffold fabricated using poly-lactic acid (PLA). The core of scaffold was composed of hyaluronic acid (HA), copper carbon dots (Cu-CDs), rosmarinic acid, and chitosan hydrogel. Cu-CDs were synthesized using ammonium hydrogen citrate under hydrothermal conditions. Formulation containing 1 mg ml^-1 concentration of Cu-CDs showed an excellent antibacterial activity against gram bacteria. At 0.25 mg ml^-1 of Cu-CDs concentration, scaffold had a good biocompatibility as confirmed by cytotoxicity assay on L929 fibroblast stem cells. in vivo wound healing experiments on groups of rats revealed that after 15 days of treatment, the optimal formulation of composite scaffold significantly improves the wound healing process compared to the PLA scaffold. This finding was confirmed by histological analysis and the relative expression of PDGF, TGF-β, and MMP-1 genes. The biocompatible antibacterial CU-CDS/PLA/HA/chitosan/rosmarinic acid nanocomposite is a promising wound healing scaffold which highly accelerates the process of skin regeneration.

Self-defensive antimicrobial biomaterial surfaces

Self-defensive biomaterial surfaces are being developed in order to mitigate infection associated with tissue-contacting biomedical devices. Such infection occurs when microbes colonize the surface of a device and proliferate into a recalcitrant biofilm. A key intervention point centers on preventing the initial colonization. Incorporating antimicrobials within a surface coating can be very effective, but the traditional means of antimicrobial delivery by continuous elution can often be counterproductive. If there is no infection, continuous elution creates conditions that promote the development of resistant microbes throughout the patient. In contrast, a self-defensive coating releases antimicrobial only when and only where there is a microbial challenge to the surface. Otherwise, the antimicrobial remains sequestered within the coating and does not contribute to the development of resistance. A self-defensive surface requires a local trigger that signals the microbial challenge. Three such triggers have been identified as: (1) local pH lowering; (2) local enzyme release; and (3) direct microbial-surface contact. This short review highlights the need for self-defensive surfaces in the general context of the device-infection problem and then reviews key biomaterials developments associated with each of these three triggering mechanisms.

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Background

Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological trade-offs can provide invaluable information regarding the biophysical and biochemical bases behind observed cellular phenotypes. A quantitative knowledge of a cell system’s critical objectives is also needed for engineering of cellular metabolism, where there is interest in mitigating the fitness costs that may result from human manipulation.

Results

To study metabolism in photoheterotrophs, we developed and validated a genome-scale model of metabolism in Rhodopseudomonas palustris, a metabolically versatile gram-negative purple non-sulfur bacterium capable of growing phototrophically on various carbon sources, including inorganic carbon and aromatic compounds. To quantitatively assess trade-offs among a set of important biological objectives during different metabolic growth modes, we used our new model to conduct an 8-dimensional multi-objective flux analysis of metabolism in R. palustris. Our results revealed that phototrophic metabolism in R. palustris is light-limited under anaerobic conditions, regardless of the available carbon source. Under photoheterotrophic conditions, R. palustris prioritizes the optimization of carbon efficiency, followed by ATP production and biomass production rate, in a Pareto-optimal manner. To achieve maximum carbon fixation, cells appear to divert limited energy resources away from growth and toward CO₂ fixation, even in the presence of excess reduced carbon. We also found that to achieve the theoretical maximum rate of biomass production, anaerobic metabolism requires import of additional compounds (such as protons) to serve as electron acceptors. Finally, we found that production of hydrogen gas, of potential interest as a candidate biofuel, lowers the cellular growth rates under all circumstances.

Conclusions

Photoheterotrophic metabolism of R. palustris is primarily regulated by the amount of light it can absorb and not the availability of carbon. However, despite carbon’s secondary role as a regulating factor, R. palustris’ metabolism strives for maximum carbon efficiency, even when this increased efficiency leads to slightly lower growth rates.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2844-z) contains supplementary material, which is available to authorized users.

Wound dressing application of pH-sensitive carbon dots/chitosan hydrogel

Monitoring the pH of wounds as an essential diagnosis factor during the healing process.

Organic Acids Regulation of Chemical-Microbial Phosphorus Transformations in Soils

We have used an integrated approach to study the mobility of inorganic phosphorus (P) from soil solid phase as well as the microbial biomass P and respiration at increasing doses of citric and oxalic acid in two different soils with contrasting agronomic P status. Citric or oxalic acids significantly increased soil solution P concentrations for doses over 2 mmol kg^-1. However, low organic acid doses (<2 mmol kg^-1) were associated with a steep increase in microbial biomass P, which was not seen for higher doses. In both soils, treatment with the tribasic citric acid led to a greater increase in soil solution P than the dibasic oxalic acid, likely due to the rapid degrading of oxalic acids in soils. After equilibration of soils with citric or oxalic acids, the adsorbed-to-solution distribution coefficient (K_d) and desorption rate constants (k_-1) decreased whereas an increase in the response time of solution P equilibration (T_c) was observed. The extent of this effect was shown to be both soil and organic acid specific. Our results illustrate the critical thresholds of organic acid concentration necessary to mobilize sorbed and precipitated P, bringing new insight on how the exudation of organic acids regulate chemical-microbial soil phosphorus transformations.

Nanoparticle-based measurements of pH and O2 dynamics in the rhizosphere of Zostera marina L.: effects of temperature elevation and light-dark transitions

Seagrasses can modulate the geochemical conditions in their immediate rhizosphere through the release of chemical compounds from their below-ground tissue. This is a vital chemical defence mechanism, whereby the plants detoxify the surrounding sediment. Using novel nanoparticle-based optical O2 and pH sensors incorporated in reduced and transparent artificial sediment, we investigated the spatio-temporal dynamics of pH and O2 within the entire rhizosphere of Zostera marina L. during experimental manipulations of light and temperature. We combined such measurements with O2 microsensor measurements of the photosynthetic productivity and respiration of seagrass leaves. We found pronounced pH and O2 microheterogeneity within the immediate rhizosphere of Z. marina, with higher below-ground tissue oxidation capability and rhizoplane pH levels during both light exposure of the leaf canopy and elevated temperature, where the temperature-mediated stimuli of biogeochemical processes seemed to predominate. Low rhizosphere pH microenvironments appeared to correlate with plant-derived oxic microzones stimulating local sulphide oxidation and thus driving local proton generation, although the rhizoplane pH levels generally where much higher than the bulk sediment pH. Our data show that Z. marina can actively alter its rhizosphere pH microenvironment alleviating the local H2 S toxicity and enhancing nutrient availability in the adjacent sediment via geochemical speciation shift.

Fine Tuning of Redox Networks on Multiheme Cytochromes from Geobacter sulfurreducens Drives Physiological Electron/Proton Energy Transduction

The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e(-)/H(+) coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e(-)/H(+) transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e(-)/H(+) transfer at the physiological pH range for cellular growth.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.