Enhanced Biocide Treatments with D-amino Acid Mixtures against a Biofilm Consortium from a Water Cooling Tower

A New Convenient Method to Assess Antibiotic Resistance and Antimicrobial Efficacy against Pathogenic Clostridioides difficile Biofilms

Clostridioides difficile is a widely distributed anaerobic pathogen. C. difficile infection is a serious problem in healthcare. Its biofilms have been found to exhibit biocorrosivity, albeit very little, but sufficient for it to correlate with biofilm growth/health. This work demonstrated the use of a disposable electrochemical biofilm test kit using two solid-state electrodes (a 304 stainless steel working electrode, and a graphite counter electrode, which also served as the reference electrode) in a 10 mL serum vial. It was found that the C. difficile 630∆erm Adp-4 mutant had a minimum inhibitory concentration (MIC) for vancomycin twice that of the 630∆erm wild type strain in biofilm prevention (2 ppm vs. 1 ppm by mass) on 304 stainless steel. Glutaraldehyde, a commonly used hospital disinfectant, was found ineffective at 2% (w/w) for the prevention of C. difficile 630∆erm wild type biofilm formation, while tetrakis(hydroxymethyl)phosphonium sulfate (THPS) disinfectant was very effective at 100 ppm for both biofilm prevention and biofilm killing. These antimicrobial efficacy data were consistent with sessile cell count and biofilm imaging results. Furthermore, the test kit provided additional transient biocide treatment information. It showed that vancomycin killed C. difficile 630∆erm wild type biofilms in 2 d, while THPS only required minutes.

A multifunctional protein-based hydrogel with Au nanozyme-mediated self generation of H2S for diabetic wound healing

Diabetics usually suffer from chronic impaired wound healing due to facile infection, excessive inflammation, diabetic neuropathy, and peripheral vascular disease. Hence, the development of effective diabetic wound therapy remains a critical clinical challenge. Hydrogen sulfide (H2S) regulates inflammation, oxidative stress, and angiogenesis, suggesting a potential role in promoting diabetic wound healing. Herein, we propose a first example of fabricating an antibiotic-free antibacterial protein hydrogel with self-generation of H2S gas (H2S-Hydrogel) for diabetic wound healing by simply mixing bovine serum albumin‑gold nanoclusters (BSA-AuNCs) with Bis[tetrakis(hydroxymethyl)phosphonium] sulfate (THPS) at room temperature within a few minutes. In this process, the amino group in BAS and the aldehyde group in THPS are crossed together by Mannich reaction. At the same time, tris(hydroxymethyl) phosphorus (trivalent phosphorus) from THPS hydrolysis could reduce disulfide bonds in BSA to sulfhydryl groups, and then the sulfhydryl group generates H2S gas under the catalysis of BSA-AuNCs. THPS in H2S-Hydrogel can destroy bacterial biofilms, while H2S can inhibit oxidative stress, promote proliferation and migration of epidermal/endothelial cells, increase angiogenesis, and thus significantly increase wound closure. It would open a new perspective on the development of effective diabetic wound dressing.

D-tryptophan, an eco-friendly natural, safe, and healthy compound with antimicrobial activity against food-borne pathogens: A systematic review

Recently, the use of D-amino acids as food preservatives has attracted considerable attention because these natural compounds do not have adverse effects on human health. In addition, D-amino acids such as D-tryptophan can reduce the harmful effects of other treatments. For instance, the use of D-tryptophan in food reduces the requirement for high temperatures and their damaging effects on nutrients such as proteins and vitamins. The purpose of this systematic review was to investigate the antimicrobial effect of D-tryptophan on food-borne pathogens in vitro and in food models. To identify related studies, scientific digital databases such as PubMed, Science Direct, and Google Scholar were searched from January 2000 to February 2023. The results of the studies showed that when D-tryptophan was used with other stresses such as using different salt concentrations, refrigeration, or high temperatures, it showed significant antimicrobial effects on Gram-positive and Gram-negative food-borne pathogens, and antibiofilm impacts were also observed with D-tryptophan. Since studies have shown that the antimicrobial activity of D-tryptophan depends on several factors, including the pathogen strain, the type of stress, and the concentration of D-tryptophan, and every article has focused on one of these factors, there is a need for a systematic review that summarizes and concludes the effect of all these factors on the antimicrobial activity of D-tryptophan against food-borne pathogens.

D-histidine combated biofilm formation and enhanced the effect of amikacin against Pseudomonas aeruginosa in vitro

Pseudomonas aeruginosa is an opportunistic gram-negative pathogenic microorganism that poses a significant challenge in clinical treatment. Antibiotics exhibit limited efficacy against mature biofilm, culminating in an increase in the number of antibiotic-resistant strains. Therefore, novel strategies are essential to enhance the effectiveness of antibiotics against Pseudomonas aeruginosa biofilms. D-histidine has been previously identified as a prospective anti-biofilm agent. However, limited attention has been directed towards its impact on Pseudomonas aeruginosa. Therefore, this study was undertaken to explore the effect of D-histidine on Pseudomonas aeruginosa in vitro. Our results demonstrated that D-histidine downregulated the mRNA expression of virulence and quorum sensing (QS)-associated genes in Pseudomonas aeruginosa PAO1 without affecting bacterial growth. Swarming and swimming motility tests revealed that D-histidine significantly reduced the motility and pathogenicity of PAO1. Moreover, crystal violet staining and confocal laser scanning microscopy demonstrated that D-histidine inhibited biofilm formation and triggered the disassembly of mature biofilms. Notably, D-histidine increased the susceptibility of PAO1 to amikacin compared to that in the amikacin-alone group. These findings underscore the efficacy of D-histidine in combating Pseudomonas aeruginosa by reducing biofilm formation and increasing biofilm disassembly. Moreover, the combination of amikacin and D-histidine induced a synergistic effect against Pseudomonas aeruginosa biofilms, suggesting the potential utility of D-histidine as a preventive strategy against biofilm-associated infections caused by Pseudomonas aeruginosa.

Biomineralization To Prevent Microbially Induced Corrosion on Concrete for Sustainable Marine Infrastructure

Microbially induced corrosion (MIC) on concrete represents a serious issue impairing the lifespan of coastal/marine infrastructure. However, currently developed concrete corrosion protection strategies have limitations in wide applications. Here, a biomineralization method was proposed to form a biomineralized film on concrete surfaces for corrosion inhibition. Laboratory seawater corrosion experiments were conducted under different conditions [e.g., chemical corrosion (CC), MIC, and biomineralization for corrosion inhibition]. A combination of chemical and mechanical property measurements of concrete (e.g., sulfate concentrations, permeability, mass, and strength) and a genotypic-based investigation of formed concrete biofilms was conducted to evaluate the effectiveness of the biomineralization approach on corrosion inhibition. The results show that MIC resulted in much higher corrosion rates than CC. However, the biomineralization treatment effectively inhibited corrosion because the biomineralized film decreased the total and relative abundance of sulfate-reducing bacteria (SRB) and acted as a protective layer to control the diffusion of sulfate and isolate the concrete from the corrosive SRB communities, which helps extend the lifespan of concrete structures. Moreover, this technique had no negative impact on the native marine microbial communities. Our study contributes to the potential application of biomineralization for corrosion inhibition to achieve long-term sustainability for major marine concrete structures.

Mitigation of EH36 ship steel biocorrosion using an antimicrobial peptide as a green biocide enhancer

In this study, a 13-mer antimicrobial peptide (RRWRIVVIRVRRC) named by E6 was used as an enhancer of a green biocide to mitigate the biocorrosion of EH36 ship steel. Results show that a low concentration of E6 (100 nM) alone was no-biocidal and could not resist the Desulfovibrio vulgaris adhesion on the EH36 steel surface. However, E6 enhanced the bactericidal effect of tetrakis hydroxymethyl phosphonium sulfate (THPS). When E6 and THPS were both added to the bacteria and steel system, both the sessile D. vulgaris cells and biocorrosion rate of EH36 steel decreased significantly. Compared with the 80 ppm THPS alone treatment, the combination of 100 nM E6 + 80 ppm THPS led to an extra 1.6-log reduction in the sessile cell count. Fewer sessile D. vulgaris cells led to a lower extracellular electron transfer (EET) rate, directly resulting in 78% and 83% decreases in weight loss and pit depth of EH36 steel, respectively. E6 saved more than 50% of THPS dosage in this work to achieve a similar biocorrosion mitigation effect on EH36 steel.

Burning question: Are there sustainable strategies to prevent microbial metal corrosion?

The global economic burden of microbial corrosion of metals is enormous. Microbial corrosion of iron-containing metals is most extensive under anaerobic conditions. Microbes form biofilms on metal surfaces and can directly extract electrons derived from the oxidation of Fe0 to Fe2+ to support anaerobic respiration. H2 generated from abiotic Fe0 oxidation also serves as an electron donor for anaerobic respiratory microbes. Microbial metabolites accelerate this abiotic Fe0 oxidation. Traditional strategies for curbing microbial metal corrosion include cathodic protection, scrapping, a diversity of biocides, alloys that form protective layers or release toxic metal ions, and polymer coatings. However, these approaches are typically expensive and/or of limited applicability and not environmentally friendly. Biotechnology may provide more effective and sustainable solutions. Biocides produced with microbes can be less toxic to eukaryotes, expanding the environments for potential application. Microbially produced surfactants can diminish biofilm formation by corrosive microbes, as can quorum-sensing inhibitors. Amendments of phages or predatory bacteria have been successful in attacking corrosive microbes in laboratory studies. Poorly corrosive microbes can form biofilms and/or deposit extracellular polysaccharides and minerals that protect the metal surface from corrosive microbes and their metabolites. Nitrate amendments permit nitrate reducers to outcompete highly corrosive sulphate-reducing microbes, reducing corrosion. Investigation of all these more sustainable corrosion mitigation strategies is in its infancy. More study, especially under environmentally relevant conditions, including diverse microbial communities, is warranted.

Electrochemical Assessment of Mitigation of Desulfovibrio ferrophilus IS5 Corrosion against N80 Carbon Steel and 26Cr3Mo Steel Using a Green Biocide Enhanced by a Nature-Mimicking Biofilm-Dispersing Peptide

MIC (microbiologically influenced corrosion) is problematic in many industries, especially in the oil and gas industry. In this work, N80 carbon steel for pipelines was tested with 26Cr3Mo chromium pipeline steel for comparison in SRB (sulfate-reducing bacterium) MIC mitigation using a THPS (tetrakis hydroxymethyl phosphonium sulfate)-based commercial biocide (Biotreat 5475 with 75-80% THPS by mass). Peptide A, a nature-mimicking synthetic cyclic peptide (cys-ser-val-pro-tyr-asp-tyr-asn-trp-tyr-ser-asn-trp-cys) with biofilm dispersal ability was used as a biocide enhancer. Metal coupons covered with 3-d old Desulfovibrio ferrophilus IS5 biofilms were immersed in different biocide solutions. After 1-h treatment, 200 ppm Biotreat 5475, 200 ppm Biotreat 5475 + 200 nM (360 ppb) Peptide A, and 400 ppm Biotreat 5475 achieved 0.5-log, 1.7-log and 1.9-log reductions in sessile cell count on N80, and 0.7-log, 1.7-log, and 1.8-log on 26Cr3Mo, respectively. The addition of 200 nM Peptide A cut the THPS biocide dosage by nearly half. Biocide injection tests in electrochemical glass cells after 1 h exhibited 15%, 70%, and 72% corrosion inhibition efficiency (based on corrosion current density) on N80, and 27%, 79%, 75% on 26Cr3Mo, respectively. Linear polarization resistance and electrochemical impedance spectrometry results also indicated antimicrobial efficacies.

Optimization of antimicrobial peptides for the application against biocorrosive bacteria

Microbiologically influenced corrosion is a common problem in the industrial field due to the deterioration of metals in the presence of various microorganisms, in particular sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB). A common method to reduce microbiologically influenced corrosion is the application of biocides. The limited number of suitable biocides and the resulting development of resistance, high dosage, and high application rate hinder an effective application. An environmentally friendly alternative could be the application of antimicrobial peptides (AMP), which have already been established in the field of medical devices for a while. Here, the successful treatment of different AMPs against 3 SRB and 1 SOB was demonstrated. The peptide L5K5W was favored due to its broad activity, high stability, and simple structure resulting in low synthesis costs. An alanine scan showed that substitution of leucine with tryptophan increased the activity of this peptide twofold compared to the original peptide against D. vulgaris, the main representative of SRB. Additional optimization of this modified peptide through changes in amino acid composition and lipidations significantly increased the effectiveness, finally resulting in a minimum inhibitory concentration (MIC) of 15.63 μg/mL against Desulfovibrio vulgaris. Even against the marine SRB Desulfovibrio indonesiensis with a required salt concentration of min. 2%, an activity of the peptides can be observed (MIC: 31.25 μg/mL). The peptides also remained stable and active for 7 days in the supernatant of the bacterial culture. KEY POINTS: • Antimicrobial peptides provide an alternative to combat biocorrosive bacteria. • Optimization of the peptide sequence leads to a significant increase in activity. • The investigated peptides exhibit high stability, both in the medium and in the bacterial supernatant.

A facile and general method for synthesis of antibiotic-free protein-based hydrogel: Wound dressing for the eradication of drug-resistant bacteria and biofilms

Antibacterial protein hydrogels are receiving increasing attention in the aspect of bacteria-infected-wound healing. However, bacterial drug resistance and biofilm infections lead to hard healing of wounds, thus the construction of biological agents that can overcome these issues is essential. Here, a simple and universal method to construct antibiotic-free protein hydrogel with excellent biocompatibility and superior antibacterial activity against drug-resistant bacteria and biofilms was developed. The green industrial microbicide tetrakis (hydroxymethyl) phosphonium sulfate (THPS) as cross-linking agent can be quickly cross-linked with model protein bovine serum albumin (BSA) to form antibacterial hydrogel through simple mixing without any other initiators, subsequently promoting drug-resistance bacteria-infected wound healing. This simple gelatinization strategy allows at least ten different proteins to form hydrogels (e.g. BSA, human serum albumin (HSA), egg albumin, chymotrypsin, trypsin, lysozyme, transferrin, myohemoglobin, hemoglobin, and phycocyanin) under the same conditions, showing prominent universality. Furthermore, drug-resistance bacteria and biofilm could be efficiently destroyed by the representative BSA hydrogel (B-Hydrogel) with antibacterial activity, overcoming biofilm-induced bacterial resistance. The in vivo study demonstrated that the B-Hydrogel as wound dressing can promote reepithelization to accelerate the healing of methicillin-resistant staphylococcus aureus (MRSA)-infected skin wounds without inducing significant side-effect. This readily accessible antibiotic-free protein-based hydrogel not only opens an avenue to provide a facile, feasible and general gelation strategy, but also exhibits promising application in hospital and community MRSA disinfection and treatment.

YgeA is involved in L- and D-homoserine metabolism in Escherichia coli

Noncanonical D-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria. Previously, we identified amino acid racemases with broad substrate specificity, including YgeA from Escherichia coli, which strongly prefers homoserine as a substrate. In this study, we investigated the functions of this enzyme in vivo. When wild-type and ygeA-deficient E. coli strains were cultured in minimal medium containing D-homoserine, the D-homoserine level was significantly higher in the ygeA-deficient strain than in the wild-type strain, in which it was almost undetectable. Additionally, D-homoserine was detected in YgeA-expressed E. coli cells cultured in minimal medium containing L-homoserine. The growth of the ygeA-deficient strain was significantly impaired in minimal medium with or without supplemental D-homoserine, while L-methionine, L-threonine or L-isoleucine, which are produced via L-homoserine, restored the growth impairment. Furthermore, the wild-type strain formed biofilms significantly more efficiently than the ygeA-deficient strain. Addition of L- or D-homoserine significantly suppressed biofilm formation in the wild-type strain, whereas this addition had no significant effect in the ygeA-deficient strain. Together, these data suggest that YgeA acts as an amino acid racemase and plays a role in L- and D-homoserine metabolism in E. coli.

Biocides and techniques for their encapsulation: a review

Biocides are compounds that are broadly used to protect products and equipment against microbiological damage. Encapsulation can effectively increase physicochemical stability and allow for controlled release of encapsulated biocides. We categorized microencapsulation into coacervation, sol-gel, and self-assembly methods. The former comprises internal phase separation, interfacial polymerization, and multiple emulsions, and the latter include polymersomes and layer-by-layer techniques. The focus of this review is the description of these categories based on their microencapsulation methods and mechanisms. We discuss the key features and potential applications of each method according to the characteristics of the biocide to be encapsulated, relating the solubility of biocides to the capsule-forming materials, the reactivity between them and the desired release rate. The role of encapsulation in the safety and toxicity of biocide applications is also discussed. Furthermore, future perspectives for biocide applications and encapsulation techniques are presented.

New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture

Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.

Evaluation of trehalase as an enhancer for a green biocide in the mitigation of Desulfovibrio vulgaris biocorrosion of carbon steel

Trehalase can biocatalyze the conversion of trehalose to glucose. It is an enzyme that plays an important role in biofilm formation. Thus, trehalase has been patented as a chemical for preventing and treating biofilms. Sulfate-reducing bacteria (SRB) biofilms are often found responsible for biocorrosion, also known as microbiologically infuenced corrosion (MIC), especially in the oil and gas industries and in water utilities. The MIC treatment process typically requires biocide treatment of biofilms, sometimes together with scrubbing. Owing to environmental concerns, a lower biocide dosage is desired in the treatment process. In this work, trehalase was tested as a green biocide enhancer to enhance tetrakis hydroxymethyl phosphonium sulfate (THPS) in the prevention of Desulfovibrio vulgaris MIC of C1018 carbon steel in ATCC 1249 culture medium at 37 °C. THPS is one of the most popular industrial biocides owing to its broad-spectrum efficacy and green chemical status. After 7 days of incubation in 50 mL anaerobic vials containing 40 mL culture medium at pH 7.0, the sessile cell counts indicated that 50 ppm (w/w) THPS + 30 ppm (w/w) trehalase led to an extra 5.7-fold sessile cell reduction when compared with the 50 ppm THPS alone treatment. As a consequence, the combination treatment also resulted in an extra 54% in pit depth reduction and 30% in weight loss reduction when compared with the 50 ppm THPS alone treatment (with 9.0 μm and 1.0 mg/cm²). The biofilm images corroborated the decreased sessile cell count and pitting corrosion.

Efficacy of glutaraldehyde enhancement by D-limonene in the mitigation of biocorrosion of carbon steel by an oilfield biofilm consortium

Microbiologically influenced corrosion (MIC) is one of the major corrosion threats in the oil and gas industry. It is caused by environmental biofilms. Glutaraldehyde is a popular green biocide for mitigating biofilms and MIC. This work investigated the efficacy of glutaraldehyde enhancement by food-grade green chemical D-limonene in the biofilm prevention and MIC mitigation using a mixed-culture oilfield biofilm consortium. After 7 days of incubation at 37 °C in enriched artificial seawater in 125 mL anaerobic vials, the 100 ppm (w/w) glutaraldehyde + 200 ppm D-limonene combination treatment reduced the sessile cell counts on C1018 carbon steel coupons by 2.1-log, 1.7-log, and 2.3-log for sulfate reducing bacteria, acid producing bacteria, and general heterotrophic bacteria, respectively in comparison with the untreated control. The treatment achieved 68% weight loss reduction and 78% pit depth reduction. The 100 ppm glutaraldehyde + 200 ppm D-limonene combination treatment was found more effective in biofilm prevention and MIC mitigation than glutaraldehyde and D-limonene used individually. Electrochemical tests corroborated weight loss and pit depth data trends.

Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima

The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (k_cat/K_0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.

Microbial corrosion of metals: The corrosion microbiome

Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe⁰ oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe⁰ oxidation. Microbes can consume H₂ abiotically generated from the oxidation of Fe⁰. Microbial H₂ removal makes continued Fe⁰ oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe⁰ oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H₂ as the electron carrier between Fe⁰ and cells. Direct Fe⁰-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe⁰ oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.

Antibacterial Effect of High-Purity Nisin Alone and in Combination with D-Amino Acids or Chlorhexidine in an Endodontic-Like Biofilm Model

New strategies to eradicate endodontic biofilms are needed. Therefore, we evaluated the effect of high-purity nisin alone and in combination with D-amino acids (D-AAs) or chlorhexidine (CHX) against an “endodontic-like” biofilm model. Biofilms were grown on hydroxyapatite discs for 64 h and treated with nisin, eight D-AAs mixture, nisin + eight D-AAs, 2% CHX, and nisin + 2% CHX. After the 5 min and 24 h treatments, biofilm cells were harvested and total colony-forming units were counted. Differences between groups were tested by two-way ANOVA followed by Tukey’s multiple comparisons test (p < 0.05). Nisin and D-AAs, alone or in combination, were not effective in reducing bacteria after short or long exposure times. After 5 min, treatment with 2% CHX and nisin + 2% CHX resulted in 2 and 2.4-log cell reduction, respectively, compared with the no treatment control (p < 0.001). After 24 h, 2% CHX and nisin + 2% CHX drastically reduced bacterial counts. In conclusion, high-purity nisin alone or in combination with D-AAs did not show antibacterial activity against multispecies biofilms. Moreover, combined treatment using nisin and CHX showed similar antibiofilm activity compared with the use of CHX alone.

Impact of commonly used Ag-Cu ion doses on Desulfovibrio sp.: growth and microbiologically induced corrosion against stainless steel

Ag-Cu ions in cooling water may inhibit the activity of sulfate-reducing bacteria and therefore provide solutions to microbiologically induced corrosion (MIC) problems, mainly caused by Desulfovibrio sp. To investigate this, the MIC behavior of Desulfovibrio sp. on 316L stainless steel in terms of growth and extracellular polymeric substances (EPS) production was investigated in the presence of Ag-Cu ions. Laboratory-scale systems were set up with final concentrations of 0.13 ppm Ag and 0.3 ppm Cu ions, as they are the frequently used doses for cooling waters, and operated over 720 hours. The corrosion rate was evaluated by gravimetric assay, scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) analyses. The growth of Desulfovibrio sp. was assessed by bacterial counting and EPS production. Ag-Cu ions in the biofilm were assessed by inductively coupled plasma - optical emission spectrometry (ICP-OES) and EDS-elemental mapping analyses. It was concluded that the ion concentrations used caused an increase in EPS production, especially of protein. The corrosion rate of the metal by Desulfovibrio sp. in the presence of ions was detected as being 29 times higher than that in the sterile medium with the ions after 720 hours. The results suggested that Desulfovibrio sp. exhibited more corrosive behavior in the presence of non-toxic concentrations of Ag-Cu ions.

Preliminary Investigation of Utilization of a Cellulose-Based Polymer in Enhanced Oil Recovery by Oilfield Anaerobic Microbes and its Impact on Carbon Steel Corrosion

Water injection increases reservoir pressure in enhanced oil recovery (EOR). Among other oilfield performance chemicals, an EOR polymer is added to the injection water to provide the viscosity necessary for effective displacement of viscous crude oil from the reservoir formation. However, these organic macromolecules may be degraded by microbes downhole, causing undesirable viscosity loss. The organic carbon utilization by the microbes promotes microbial metabolism, thus potentially exacerbating microbiologically influenced corrosion (MIC). In this preliminary laboratory investigation, 3,000 ppm (w/w) carboxymethyl cellulose sodium (CMCS), a commonly used EOR polymer, was found to be utilized by an oilfield biofilm consortium. This oilfield biofilm consortium consisted of bacteria (including that can degrade large organic molecules), sulfate-reducing bacteria (SRB), and other microorganisms. A 30-day incubation in 125 mL anaerobic vials was conducted with an artificial seawater medium without yeast extract and lactate supplements at 37°C. The polymer biodegradation led to 16% viscosity loss in the broth and a 30× higher SRB sessile cell count. Slightly increased MIC weight loss and pitting corrosion were observed on C1018 carbon steel coupons. Thus, the use of CMCS in EOR should take into the consideration of microbial degradation and its impact on MIC.

Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (k_cat/K_m) of TTHA1643 toward d- and l-Glu was comparable; however, the k_cat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.

Controlling biofilms using synthetic biology approaches

Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.

Decreasing microbially influenced metal corrosion using free nitrous acid in a simulated water injection system

Microbially influenced corrosion (MIC) is the main cause of metal corrosion in anoxic environments. Biocides are often dosed to the corrosive media to inhibit and kill the microbes which cause MIC. In this study, intermittent dosages of free nitrous acid (FNA), which was previously found to be a biocide, were applied to a simulated water injection system containing carbon steel coupons with mature biofilm, to study the effect of FNA on mitigation of metal corrosion. In each treatment, 0.49 mg-N/L FNA was dosed using 200 mg-N/L nitrite at pH 6 for 24 h. The corrosion properties were monitored by open circuit potential (OCP), electrochemical impedance spectroscopy (EIS), linear polarization resistance (LPR), 3D optical profiling, and direct weight measurement. The biofilm viability was monitored by measuring cellular ATP level. The general corrosion rate (calculated by weight-loss measurement) was decreased by up to 31%, which was supported by LPR tests and reduced ATP levels of the corrosion-inducing biofilm. The 3D optical profiling results showed that FNA decreased the average pitting corrosion rate by 59%, with 2 intermittent treatments and 82-day interval over 304 days. Intermittent dosing of FNA has strong potential to be an effective and efficient strategy for controlling MIC in oil recovery infrastructure.

Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical D-amino acid

Bacteria produce various D-amino acids, including non-canonical D-amino acids, to adapt to environmental changes and overcome a variety of threats. These D-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical D-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized D-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing D-Asn, D-His, or D-Trp. These D-amino acids slowed the growth of dacA- or dacB-deficient E. coli (∆dacA or ∆dacB) relative to the wild-type strain. Additionally, these D-amino acids affected biofilm formation by the ∆dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical D-amino acids, and these properties affect growth and biofilm formation.

Methicillin-resistant Staphylococcus aureus (MRSA): antibiotic-resistance and the biofilm phenotype

Staphylococcus aureus (S. aureus) is an asymptomatic colonizer of 30% of all human beings. While generally benign, antibiotic resistance contributes to the success of S. aureus as a human pathogen. Resistance is rapidly evolved through a wide portfolio of mechanisms including horizontal gene transfer and chromosomal mutation. In addition to traditional resistance mechanisms, a special feature of S. aureus pathogenesis is its ability to survive on both biotic and abiotic surfaces in the biofilm state. Due to this characteristic, S. aureus is a leading cause of human infection. Methicillin-resistant S. aureus (MRSA) in particular has emerged as a widespread cause of both community- and hospital-acquired infections. Currently, MRSA is responsible for 10-fold more infections than all multi-drug resistant (MDR) Gram-negative pathogens combined. Recently, MRSA was classified by the World Health Organization (WHO) as one of twelve priority pathogens that threaten human health. In this targeted mini-review, we discuss MRSA biofilm production, the relationship of biofilm production to antibiotic resistance, and front-line techniques to defeat the biofilm-resistance system.

Self-assembled DNA-THPS hydrogel as a topical antibacterial agent for wound healing

We report a novel and potential wound dressing hydrogel based on DNA and a green industrial microbiocide tetrakis (hydroxymethyl) phosphonium sulfate (THPS) via one-pot self-assembly. Intermolecular electrostatic interaction and hydrogen bonding between DNA and THPS together drive the formation of the adhesive DNT (DNA+THPS) hydrogel, featuring with self-healing, shear-thinning and injectability. This wound dressing hydrogel possesses broad-spectrum antibacterial ability with low cytotoxicity to L929 cells. Furthermore, the wound dressing can reduce the risk of wound infection by releasing THPS to suppress bacterial spread and accelerate wound healing. The low cost and simple preparation may make the hydrogel attractive in biomedical applications and could be a good reference to others.

Loss of Function in Escherichia coli Exposed to Environmentally Relevant Concentrations of Benzalkonium Chloride

Assessing the risk of resistance associated with biocide exposure commonly involves exposing microorganisms to biocides at concentrations close to the MIC. With the aim of representing exposure to environmental biocide residues, Escherichia coli MG1655 was grown for 20 passages in the presence or absence of benzalkonium chloride (BAC) at 100 ng/liter and 1,000 ng/liter (0.0002% and 0.002% of the MIC, respectively). BAC susceptibility, planktonic growth rates, motility, and biofilm formation were assessed, and differentially expressed genes were determined via transcriptome sequencing. Planktonic growth rate and biofilm formation were significantly reduced (P < 0.001) following BAC adaptation, while BAC minimum bactericidal concentration increased 2-fold. Transcriptomic analysis identified 289 upregulated and 391 downregulated genes after long-term BAC adaptation compared with the respective control organism passaged in BAC-free medium. When the BAC-adapted bacterium was grown in BAC-free medium, 1,052 genes were upregulated and 753 were downregulated. Repeated passage solely in biocide-free medium resulted in 460 upregulated and 476 downregulated genes compared with unexposed bacteria. Long-term exposure to environmentally relevant BAC concentrations increased the expression of genes associated with efflux and reduced the expression of genes associated with outer-membrane porins, motility, and chemotaxis. This was manifested phenotypically through the loss of function (motility). Repeated passage in a BAC-free environment resulted in the upregulation of multiple respiration-associated genes, which was reflected by increased growth rate. In summary, repeated exposure of E. coli to BAC residues resulted in significant alterations in global gene expression that were associated with minor decreases in biocide susceptibility, reductions in growth rate and biofilm formation, and loss of motility.IMPORTANCE Exposure to very low concentrations of biocides in the environment is a poorly understood risk factor for antimicrobial resistance. Repeated exposure to trace levels of the biocide benzalkonium chloride (BAC) resulted in loss of function (motility) and a general reduction in bacterial fitness but relatively minor decreases in susceptibility. These changes were accompanied by widespread changes in the Escherichia coli transcriptome. These results demonstrate the importance of including phenotypic characterization in studies designed to assess the risks of biocide exposure.

Evaluation of biocidal efficacy of Chloramine T trihydrate on planktonic and sessile bacteria in a model cooling tower water system

A model cooling tower system was experimentally seeded with Legionella pneumophila and real industrial cooling tower (CT) water has been run at the closest to full-scale system operating conditions. The water/biofilm samples were taken from the model system monthly, and the effectiveness of the different concentrations of Chloramine T trihydrate biocide was evaluated in terms of its ability to control both planktonic/sessile microbial populations. Although Chloramine T is a recommended commercial formulation for disinfecting CTs, there is a lack of published data on the efficacy of this compound against both planktonic and sessile populations in the cooling tower. Biocide response in both sessile/planktonic bacteria counts varied according to months. Tested biocide concentrations provided the clean tower conditions by reducing the concentration of heterotrophic plate count (HPC) below <10⁴ cfu mL^-1, L. pneumophila <10 cfu mL^-1 and of adenosine triphosphate (ATP) values <300 relative light units (RLU), after 1, 3 and 24 h of exposure, during a 6-month period. There were no statistically significant differences in efficacy between concentrations in terms of reduction in the number of bacteria, decrease in ATP value and viability. The results revealed that Chloramine T can effectively control biofouling in cooling systems according to the limit values of the successful control program.

Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima

Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.

Cystathionine β-lyase is involved in d-amino acid metabolism

Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.

New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems

In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr’s promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems.

Anaerobic Corrosion of 304 Stainless Steel Caused by the Pseudomonas aeruginosa Biofilm

Pseudomonas aeruginosa is a ubiquitous bacterium capable of forming problematic biofilms in many environments. They cause biocorrosion of medical implants and industrial equipment and infrastructure. Aerobic corrosion of P. aeruginosa against stainless steels has been reported by some researchers while there is a lack of reports on anaerobic P. aeruginosa corrosion in the literature. In this work, the corrosion by a wild-type P. aeruginosa (strain PAO1) biofilm against 304 stainless steel (304 SS) was investigated under strictly anaerobic condition for up to 14 days. The anaerobic corrosion of 304 SS by P. aeruginosa was reported for the first time. Results showed that the average sessile cell counts on 304 SS coupons after 7- and 14-day incubations were 4.8 × 10⁷ and 6.2 × 10⁷ cells/cm², respectively. Scanning electron microscopy and confocal laser scanning microscopy corroborated the sessile cell counts. The X-ray diffraction analysis identified the corrosion product as iron nitride, confirming that the corrosion was caused by the nitrate reducing biofilm. The largest pit depths on 304 SS surfaces after the 7- and 14-day incubations with P. aeruginosa were 3.9 and 7.4 μm, respectively. Electrochemical tests corroborated the pitting data.