The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport

The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.

Green synthesis of reduced graphene oxide by using tropical microalgae and its application in biophotovoltaic devices

The successful commercialization of algal biophotovoltaics (BPV) technology hinges upon a multifaceted approach, encompassing factors such as the development of a cost-efficient and highly conductive anode material. To address this issue, we developed an environmentally benign method of producing reduced graphene oxide (rGO), using concentrated Chlorella sp. UMACC 313 suspensions as the reducing agent. The produced rGO was subsequently coated on the carbon paper (rGO-CP) and used as the BPV device's anode. As a result, maximum power density was increased by 950% for Chlorella sp. UMACC 258 (0.210 mW m-2) and 781% for Synechococcus sp. UMACC 371 (0.555 mW m-2) compared to bare CP. The improved microalgae adhesion to the anode and improved electrical conductivity of rGO brought on by the effective removal of oxygen functional groups may be the causes of this. This study has demonstrated how microalgal-reduced GO may improve the efficiency of algal BPV for producing bioelectricity.

Inoculum and pH effects on ammonium removal and microbial community dynamics in aquaponics systems

Understanding the ecology of microorganisms is essential for optimizing aquaponics systems. Effects of pH and inoculum on ammonium removal and dynamics of microbial community composition from all compartments of lab-scale aquaponics systems were examined. Initial ammonium accumulation in systems with comammox-enriched inocula were 47% and 69% that of systems enriched with ammonia-oxidizing bacteria (AOB), with higher rates of ammonium removal and transient nitrite accumulation measured in the latter systems. By the end of operation, Nitrosomonas and Nitrosospira AOB were dominant nitrifiers in systems at pH 7.6-7.8, whereas comammox (Nitrospira) nitrifiers and plant growth-promoting microbes were abundant in systems operating at pH 5.8-6.0. Lower pH systems supported more robust plant growth with no significant effects on fish health. This study demonstrated functional redundancy of aquaponics microbiota, with selectivity of nitrifying taxa as a function of pH. The results suggest that inoculum and pH are important considerations for aquaponics system initiation and optimization.

Relative impact of three growth conditions on the Escherichia coli protein acetylome

Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).

Hermetia illucens, an innovative and sustainable source of chitosan-based coating for postharvest preservation of strawberries

The ability of chitosan produced from pupal exuviae of Hermetia illucens to retard the decay of the local strawberry (Fragaria x ananassa) cultivar Melissa was investigated for the first time in this paper. The results demonstrated the effectiveness of insect chitosan compared to the commercial polymer in preserving and enhancing, at the same time, some physicochemical parameters (weight loss, pH and soluble solids content) and nutraceutical properties (total polyphenol content, total flavonoid content and total antioxidant activity) of strawberries stored at RT, 4°C and at mixed storage conditions (4°C + RT). Moreover, chitosan from H. illucens was also effective in reducing fungal decay and improving fruit shelf life. The obtained results confirm that insect chitosan, particularly deriving from H. illucens pupal exuviae, can be a viable alternative to crustacean one in safeguarding postharvest fruits.

Bacterial cell sensing and signaling pathway for external polycyclic aromatic hydrocarbons (PAHs)

The mechanism by which a bacterial cell senses external nutrients remains largely unknown. In this study, we identified a bacterial cell sensing system for polycyclic aromatic hydrocarbons (PAHs) in a common marine PAH-using bacterium, Cycloclasticus. It consists of an outer membrane receptor (PahS) and a periplasmic protein (PahP) in combination with a two-component sensing system (TCS) that ensures a rapid response to PAH occurrence by directly controlling serial reactions including chemotactic sensing and movement, PAH uptake and intracellular PAH metabolism. PahS protrudes from the cell and acts as a PAH sensor, transducing the PAH signal across the outer membrane to its periplasmic partner PahP, which in turn transduces the PAH signal across the periplasm to a specialized TCS. This sensing system plays a critical role in sensing and promoting the metabolism of PAHs, which can be scavenged by various hydrocarbon-degrading bacteria.

Activity modulation of the Escherichia coli F1FO ATP synthase by a designed antimicrobial peptide via cardiolipin sequestering

Most antimicrobial peptides (AMPs) exert their microbicidal activity through membrane permeabilization. The designed AMP EcDBS1R4 has a cryptic mechanism of action involving the membrane hyperpolarization of Escherichia coli, suggesting that EcDBS1R4 may hinder processes involved in membrane potential dissipation. We show that EcDBS1R4 can sequester cardiolipin, a phospholipid that interacts with several respiratory complexes of E. coli. Among these, F₁F_O ATP synthase uses membrane potential to fuel ATP synthesis. We found that EcDBS1R4 can modulate the activity of ATP synthase upon partition to membranes containing cardiolipin. Molecular dynamics simulations suggest that EcDBS1R4 alters the membrane environment of the transmembrane F_O motor, impairing cardiolipin interactions with the cytoplasmic face of the peripheral stalk that binds the catalytic F₁ domain to the F_O domain. The proposed mechanism of action, targeting membrane protein function through lipid reorganization may open new venues of research on the mode of action and design of other AMPs.

COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities

Equitable SARS-CoV-2 surveillance in low-resource communities lacking centralized sewers is critical as wastewater-based epidemiology (WBE) progresses. However, large-scale studies on SARS-CoV-2 detection in wastewater from low-and middle-income countries is limited because of economic and technical reasons. In this study, wastewater samples were collected twice a month from 186 urban and rural subdistricts in nine provinces of Thailand mostly having decentralized and non-sewered sanitation infrastructure and analyzed for SARS-CoV-2 RNA variants using allele-specific RT-qPCR. Wastewater SARS-CoV-2 RNA concentration was used to estimate the real-time incidence and time-varying effective reproduction number (Re). Results showed an increase in SARS-CoV-2 RNA concentrations in wastewater from urban and rural areas 14-20 days earlier than infected individuals were officially reported. It also showed that community/food markets were "hot spots" for infected people. This approach offers an opportunity for early detection of transmission surges, allowing preparedness and potentially mitigating significant outbreaks at both spatial and temporal scales.

The soil microbiome: An essential, but neglected, component of regenerative agroecosystems

Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.

Hemisynthetic alkaloids derived from trilobine are antimalarials with sustained activity in multidrug-resistant Plasmodium falciparum

Malaria eradication requires the development of new drugs to combat drug-resistant parasites. We identified bisbenzylisoquinoline alkaloids isolated from Cocculus hirsutus that are active against Plasmodium falciparum blood stages. Synthesis of a library of 94 hemi-synthetic derivatives allowed to identify compound 84 that kills multi-drug resistant clinical isolates in the nanomolar range (median IC₅₀ ranging from 35 to 88 nM). Chemical optimization led to compound 125 with significantly improved preclinical properties. 125 delays the onset of parasitemia in Plasmodium berghei infected mice and inhibits P. falciparum transmission stages in vitro (culture assays), and in vivo using membrane feeding assay in the Anopheles stephensi vector. Compound 125 also impairs P. falciparum development in sporozoite-infected hepatocytes, in the low micromolar range. Finally, by chemical pull-down strategy, we characterized the parasite interactome with trilobine derivatives, identifying protein partners belonging to metabolic pathways that are not targeted by the actual antimalarial drugs or implicated in drug-resistance mechanisms.

Assessment of the aerobic and anaerobic biodegradation of contaminants of emerging concern in sludge using batch reactors

This work explores the degradation of xenobiotic compounds in aerobic and anaerobic batch reactors. Different inoculums were spiked with nine emerging contaminants at nominal concentrations ranging between 1 to 2 mg/L (ibuprofen, diclofenac, naproxen, acesulfame, sucralose, aspartame, cyclamate, linear alkylbenzene sulfonates, and secondary alkyl sulfonates). Ethanol was used as co-substrate in the anaerobic reactors. We found that the kinetic decay was faster in the aerobic reactors inoculated with a Spanish (S_pn) inoculum compared to a Brazilian (B_rz) inoculum, resulting in rection rates for LAS and SAS of 2.67 ± 3.6 h^-1 and 5.09 ± 6 h^-1 for the B_rz reactors, and 1.3 ± 0.1 h^-1 and 1.5 ± 0.2 h^-1 for the S_pn reactors, respectively. There was no evidence of LAS and SAS degradation under anaerobic conditions within 72 days; nonetheless, under aerobic conditions, these surfactants were removed by both the B_rz and S_pn inoculums (up to 86.2 ± 9.4% and 74.3 ± 0.7%, respectively) within 10 days. The artificial sweeteners were not removed under aerobic conditions, whereas we could observe a steady decrease in the anaerobic reactors containing the S_pn inoculum. Ethanol aided in the degradation of surfactants in anaerobic environments. Proteiniphilum, Paraclostridium, Arcobacter, Proteiniclasticum, Acinetobacter, Roseomonas, Aquamicrobium, Moheibacter, Leucobacter, Synergistes, Cyanobacteria, Serratia, and Desulfobulbus were the main microorganisms identified in this study.

Urea is a drop-in nitrogen source alternative to ammonium sulphate in Yarrowia lipolytica

Media components, including the nitrogen source, are significant cost factors in cultivation processes. The nitrogen source also influences cell behavior and production performance. Ammonium sulfate is a widely used nitrogen source for microorganisms' cultivation. Urea is a sustainable and cheap alternative nitrogen source. We investigated the influence of urea as a nitrogen source compared to ammonium sulfate by cultivating phenotypically different Yarrowia lipolytica strains in chemostats under carbon or nitrogen limitation. We found no significant coherent changes in growth and lipid production. RNA sequencing revealed no significant concerted changes in the transcriptome. The genes involved in urea uptake and degradation are not upregulated on a transcriptional level. Our findings support urea usage, indicating that previous metabolic engineering efforts where ammonium sulfate was used are likely translatable to the usage of urea and can ease the way for urea as a cheap and sustainable nitrogen source in more applications.

Rapid detection of Staphylococcus aureus and Streptococcus pneumoniae by real-time analysis of volatile metabolites

Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that secondary electrospray ionization–high resolution mass spectrometry (SESI-HRMS) can be used as a diagnostic tool for rapid detection of bacterial infections as a supportive system for current state-of-the-art diagnostics. Volatile organic compounds (VOCs) produced by growing S. aureus or S. pneumoniae cultures on blood agar plates were detected within minutes and allowed for the distinction of these two bacteria on a species and even strain level within hours. Furthermore, we obtained a fingerprint of clinical patient samples within minutes of measurement and predominantly observed a separation of samples containing live bacteria compared to samples with no bacterial growth. Further development of this technique may reduce the time required for microbiological diagnosis and should help to improve patient’s tailored treatment.

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Real-time mass spectrometry shows potential as a tool for microbiological diagnosis

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Bacterial volatile metabolites from 1 × 10³ CFUs are detected within minutes

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S. aureus and S. pneumoniae can be distinguished on species and even strain level

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Complex clinical samples cluster according to presence or absence of viable bacteria

Using structure-function relationships to understand the mechanism of phenazine-mediated extracellular electron transfer in Escherichia coli

Phenazines are redox-active nitrogen-containing heterocyclic compounds that can be produced by either bacteria or synthetic approaches. As an electron shuttles (mediators), phenazines are involved in several biological processes facilitating extracellular electron transfer (EET). Therefore, it is of great importance to understand the structural and electronic properties of phenazines that promote EET in microbial electrochemical systems. Our previous study experimentally investigated a phenazine-based library as an exogenous mediator system to facilitate EET in Escherichia coli. Herein, we combine our experimental data with density functional theory (DFT) calculations and multivariate linear regression modeling to understand the structure-function relationships in phenazine-based mediated EET. These calculations demonstrate that the computed redox properties of phenazines in lipophilic environments (e.g., cell membrane) correlate to experimental mediated current densities. Additional DFT-derived molecular properties were considered to develop a predictive model, which could be used in metabolic engineering approaches to introduce phenazines as endogenous mediators into bacteria.

Anaerobic co-digestion of agricultural wastes toward circular bioeconomy

A huge amount of agricultural wastes and waste activated-sludge are being generated every year around the world. Anaerobic co-digestion (AcD) has been considered as an alternative for the utilization of organic matters from such organic wastes by producing bioenergy and biochemicals to realize a circular bioeconomy. Despite recent advancement in AcD processes, the effect of feedstock compositions and operating conditions on the biomethane production processe has not been critically explored. In this paper, we have reviewed the effects of feedstock (organic wastes) characteristics, including particle size, carbon-to-nitrogen ratio, and pretreatment options, on the performance of an anaerobic digestion process. In addition, we provided an overview of the effect of key control parameters, including retention time, temperature, pH of digestate, volatile fatty acids content, total solids content, and organic loading rate. Lastly, based on the findings from the literature, we have presented several perspectives and prospects on priority research to promote AcD to a steppingstone for a circular bioeconomy.

The impact of propagule pressure on whole community invasions in biomethane-producing communities

Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.

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Complex communities can successfully invade other communities

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Invasions change the community composition independently of propagule pressure

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Number of taxa invading increases with increased propagule pressure

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Larger propagule pressure impacts both the community structure and function

Enhancing polypropylene bioconversion and lipogenesis by Yarrowia lipolytica using a chemical/biological hybrid process

Plastic waste can serve as a feedstock for microbial bioconversion using a chemical/biological hybrid strategy. We developed a polypropylene (PP) upcycling process that coupled pyrolysis with bioconversion by the oleaginous yeast Yarrowia lipolytica. Using virgin PP, we optimized pH, inoculum density, C/N ratio, and osmolarity and increased the fatty acid titer nearly four-fold to 1.9 g L^-1, with 41 percent cellular fatty acid content, the highest content reported to date for plastic-to-lipid microbial bioconversion. The highest fatty acid titer was achieved with an inoculum density of 3 (OD 600 nm), pH = 6.0 and C/N ratio of 80:1. Increasing the medium osmolarity by adding sodium chloride adversely affected cell growth and did not improve the fatty acid titer. The maximum fatty acid titer occurred under conditions that balanced cell growth versus lipogenesis. Using postconsumer PP, the fatty acid titer was significantly lower (0.13 g L^-1). Overall, the work demonstrates the potential and the challenges associated with microbial bioconversion of plastics.

The potential application of probiotics and prebiotics for the prevention and treatment of COVID-19

COVID-19 is a pandemic disease caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new viral infection was first identified in China in December 2019, and it has subsequently spread globally. The lack of a vaccine or curative treatment for COVID-19 necessitates a focus on other strategies to prevent and treat the infection. Probiotics consist of single or mixed cultures of live microorganisms that can beneficially affect the host by maintaining the intestinal or lung microbiota that play a major role in human health. At present, good scientific evidence exists to support the ability of probiotics to boost human immunity, thereby preventing colonization by pathogens and reducing the incidence and severity of infections. Herein, we present clinical studies of the use of probiotic supplementation to prevent or treat respiratory tract infections. These data lead to promising benefits of probiotics in reducing the risk of COVID-19. Further studies should be conducted to assess the ability of probiotics to combat COVID-19.

Nanosecond electric pulses rapidly enhance the inactivation of Gram-negative bacteria using Gram-positive antibiotics

Physically disrupting microorganism membranes to enable antibiotics to overcome resistance mechanisms that inhibit or excrete antibiotics has great potential for reducing antibiotic doses and rendering resistance mechanisms inert. We demonstrate the synergistic inactivation of a Gram-positive (Staphylococcus aureus) and two Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria by combining 222 30 kV/cm electric pulses (EPs) or 500 20 kV/cm EPs with 300-ns EP duration with various antibiotics with different mechanisms of action is demonstrated. Doses of antibiotics that produced no inactivation in 10 min of exposure in solution with bacteria induced several log reductions under the influence of nanosecond EPs. Combining 2 μg/L or 20 μg/mL of rifampicin with the 30 kV/cm EPs enhanced Staphylococcus aureus inactivation compared with EPs alone, while only a few of the other combinations demonstrated improvement. Combining 2 μg/L or 20 μg/mL of mupirocin or rifampicin with either EP train enhanced E. coli inactivation compared with EPs alone. Combining 2 μg/L or 20 μg/mL of erythromycin or vancomycin with the 30 kV/cm EPs enhanced E. coli inactivation compared with EPs alone. These results indicate that EPs can make Gram-positive antibiotics efficient for inactivating Gram-negative bacteria with future studies required to optimize EP parameters for other antibiotics and Gram-negative bacteria.

Erratum: Publisher Correction: A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound

[This corrects the article DOI: 10.1038/s42003-019-0676-z.].

Microbial biofilm formation and degradation of octocrylene, a UV absorber found in sunscreen

Octocrylene is a widely used synthetic UV absorber of sunscreens and found in several environments. Ecological consequences of the accumulation of UV filters are widely discussed. This is the first report revealing the microbial potential to transform octocrylene. A microbial community comprising four bacterial species was enriched from a landfill site using octocrylene as carbon source. From these microorganisms Mycobacterium agri and Gordonia cholesterolivorans were identified as most potent applying a new "reverse discovery" approach. This relies on the possibility that efficient strains that are already isolated and deposited can be identified through enrichment cultures. These strains formed massive biofilms on the octocrylene droplets. GC-MS analysis after cultivation for 10 days with M. agri revealed a decrease in octocrylene concentration of 19.1%. LC-MS/MS analysis was utilized in the detection and quantification of transformation products of octocrylene. M. agri thus represents an ideal candidate for bioremediation studies with octocrylene and related compounds.

A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound

TonB-dependent receptors (TBDRs) mediate substrate-specific transport across the outer membrane, utilizing energy derived from the proton motive force transmitted from the TonB-ExbB-ExbD complex located in the inner membrane (TonB system). Although a number of TonB systems involved in the uptake of siderophores, vitamin B12 and saccharides have been identified, their involvement in the uptake and catabolism of aromatic compounds was previously unknown. Here, we show that the outer membrane transport of a biphenyl compound derived from lignin is mediated by the TonB system in a Gram-negative bacterium capable of degrading lignin-derived aromatic compounds, Sphingobium sp. strain SYK-6. Furthermore, we found that overexpression of the corresponding TBDR gene enhanced the uptake of this biphenyl compound, contributing to the improved rate of platform chemical production. Our results will provide an important basis for establishing engineered strains optimized for use in lignin valorisation.

Development of a high-productivity, halophilic, thermotolerant microalga Picochlorum renovo

Microalgae are promising biocatalysts for applications in sustainable fuel, food, and chemical production. Here, we describe culture collection screening, down-selection, and development of a high-productivity, halophilic, thermotolerant microalga, Picochlorum renovo. This microalga displays a rapid growth rate and high diel biomass productivity (34 g m-2 day-1), with a composition well-suited for downstream processing. P. renovo exhibits broad salinity tolerance (growth at 107.5 g L-1 salinity) and thermotolerance (growth up to 40 °C), beneficial traits for outdoor cultivation. We report complete genome sequencing and analysis, and genetic tool development suitable for expression of transgenes inserted into the nuclear or chloroplast genomes. We further evaluate mechanisms of halotolerance via comparative transcriptomics, identifying novel genes differentially regulated in response to high salinity cultivation. These findings will enable basic science inquiries into control mechanisms governing Picochlorum biology and lay the foundation for development of a microalga with industrially relevant traits as a model photobiology platform.

Cetylpyridinium chloride produces increased zeta-potential on Salmonella Typhimurium cells, a mechanism of the pathogen's inactivation

Cetylpyridinium chloride (CPC) is a quaternary ammonium sanitizer approved for fresh poultry animal carcass sanitization from microbial human pathogens, such as Salmonella enterica. Nonetheless, the interactions of CPC with Salmonella cells, and the mechanism of the sanitizer's neutralization by lecithin remains largely unknown. This study aimed to investigate the interaction of CPC with lecithin and Salmonella Typhimurium to determine the interactions of the sanitizer and neutralizer impacting the bacterium's survival. Application of 0.8% CPC is proposed to produce loss of microbial membrane integrity with loss of electrostatic repulsion between individual cells, resulting in the eventual emulsification of membrane lipids with cytoplasmic contents leakage. Our findings point to a two-phase interaction between CPC and lecithin impacting S. Typhimurium survival. The first consists of electrostatic attraction and charge neutralization between oppositely charged components of pathogen cell and CPC. The second involves formation of aggregates between sanitizer and pathogen, or between sanitizer, pathogen membrane lipids, and lecithin.

Trophic networks improve the performance of microbial anodes treating wastewater

Microbial anodes represent a distinct ecological niche that is characterized mainly by the terminal electron acceptor, i.e., the anode potential, and the substrate, i.e., the electron source. Here, we determine the performance and the biofilm community of anode microbiomes while using substrates of increasing complexity (organic acids or organic acids and sugar or real domestic wastewater) to mimic different, practically relevant, trophic levels. α-Diversity values increased with substrate complexity. In addition, the higher abundance value of Deltaproteobacteria in the biofilms corresponds to higher reactor performance (i.e., COD removal, current density, and Coulombic efficiency). In reactors exploiting real wastewater, the diversity of the planktonic microorganisms was only little affected. Microbiome network analysis revealed two important clusters for reactor performance as well as performance-independent pathogen-containing clusters. Interestingly, Geobacter was not found to be integrated in the network underlining its outstanding individual ecological role in line with its importance for the efficiency of the electron harvest for all reactors. The microbiome analysis of different trophic levels and their temporal development from initial colonization to stable treatment demonstrate important principles for the implementation of microbial anodes for wastewater treatment.

Discovery of Potential Genes Contributing to the Biosynthesis of Short-Chain Fatty Acids and Lactate in Gut Microbiota From Systematic Investigation in. NPJ Biofilms Microbiomes. 2019;12:19. [PMID: 31312512 PMCID: PMC6626047 DOI: 10.1038/s41522-019-0092-7]

Microbiota play important roles in the internal environment and health of humans, livestock and wild animals. Short-chain fatty acids (SCFAs) and lactate are primary metabolites that can impact the composition and function of human microbiota. According to the well-characterized key synthesis genes, many SCFA- and lactate-producing bacteria have been identified in the gut microbiota. However, unknown genes may also contribute to the formation of SCFAs and lactate. The identification of such genes will provide new engineering targets and new strategies for maintaining a stable structure of beneficial microbiota. In this study, we used Escherichia coli as a model to analyze possible genes related to SCFAs and lactate production besides the well-characterized ones. The functions of nineteen candidate genes were studied by targeted gene deletion and overexpression. Results indicated thioesterase genes such as yciA, tesA, tesB, and menI can contribute to acetate and/or butyrate formation. As for lactate, mgsA and lldD can function in addition to ldh gene. At the same time, the distribution of these functional genes in gut microbiota was investigated. Most bacteria contain the well-studied genes whereas some bacteria contain some of the described unusual ones. The results provide insights and genetic targets for the discovery of new SCFA- and lactate-producing bacteria in gut microbiota.

MS2 coliphage inactivation by Al/Fe PILC-activated Catalytic Wet Peroxide Oxidation: multiresponse statistical optimization

The optimization of the Catalytic Wet Peroxide Oxidation (CWPO) assisted by an Al/Fe-pillared clay (Al/Fe-PILC) was assessed in the inactivation of the MS2 coliphage in the presence of a synthetic surrogate of natural organic matter (NOM). The simultaneous effect of two experimental factors (i) H₂O₂ dose - (H₂O₂)_d (3.00-25.50 % of the H₂O₂ theoretically required for full mineralization) and (ii) catalyst concentration (0.33-2.60 g/L), and four non-controllable variables (covariates) (a) circumneutral pH (6.00-9.00), (b) temperature (5.00-25.0 °C), (c) synthetic NOM concentration (2.0-20.0 mg C/L) and (d) MS2 titer (10⁴, 10⁵ and 10⁶ PFU/mL) was investigated by Response Surface Methodology (RSM). Every response was modeled and maximized: (1) MS2 inactivation, (2) fraction of reacted H₂O₂, (3) decolourization and (4) NOM mineralization. Multi-response optimization via desirability function based on responses (1) to (3) achieved excellent fitting (0.94 out of 1.0) and following set of optimal experimental conditions: 0.33 g Al/Fe-PILC/L, 3.36 % (H₂O₂)_d ​(Fe_active/H₂O₂) = 0.46, giving rise to 92.9 % of MS2 inactivation and 100 % of reacted H₂O₂ at pH 7.07, 25.0 +/- 0.1 °C, 16.06 mg C/L as starting NOM concentration, and MS2 titer of 10⁶ PFU/mL after just 70 min ​of reaction.

Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis

Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, can be viewed together through the lens of electrochemical bioreactor technology in order to highlight the challenges that exist in creating a versatile platform technology for use in chemical and biological applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations often necessitate convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor, NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via electrochemical reduction is motivated by the low cost of performing electrochemical reactions, easy monitoring of the reaction progress, and straightforward product recovery. However, electrochemical cofactor regeneration methods invariably produce adventitious reduced cofactor side products which result in unproductive loss of input NAD(P). Microbial electrosynthesis is a form of microbially driven catalysis in which electricity is supplied to living microorganisms for the production of industrially relevant chemical products at higher carbon efficiencies and yields compared with traditional, nonelectrically driven, fermentations. The fundamental biochemistry of these organisms as related to selected biochemical redox processes will be explored in order to highlight opportunities to devise strategies for taking advantage of these biochemical processes in engineered systems.

Synergistic bacterial inactivation by combining antibiotics with nanosecond electric pulses

Antibiotic resistance mechanisms render current antibiotics ineffective, requiring higher concentrations of existing drugs or the development of more powerful drugs for infection treatment. This study demonstrates the synergistic inactivation of a gram-positive (Staphylococcus aureus) and a gram-negative (Escherichia coli) bacteria by combining either tobramycin or rifampicin with 300-ns electric pulses (EPs). For EPs depositing the same total energy density into the sample with no drug, higher electric fields induced greater inactivation, indicating a threshold for irreversible electroporation at these fields and membrane recovery in between lower intensity EPs. Synergistic inactivation generally increased with increasing drug concentration up to 20 μg/mL compared to strictly EP treatment. Combining even 1/20 of the clinical dose of tobramycin with a train of EPs induced between 2.5 and 3.5 log inactivation after only 10 min of exposure compared to hours to induce inactivation with a clinical dose with no EPs. Similarly, combining a train of EPs with a clinically relevant dose of rifampicin induced 7 to 9 log inactivation over the same time of exposure. These results indicate the promise of combining EPs with antibiotics to rapidly inactivate antibiotic-resistant bacteria in localized treatment areas.

Microbial production of toxins from the scorpion venom: properties and applications

Scorpion venom are composed mainly of bioactive proteins and peptides that may serve as lead compounds for the design of biotechnological tools and therapeutic drugs. However, exploring the therapeutic potential of scorpion venom components is mainly impaired by the low yield of purified toxins from milked venom. Therefore, production of toxin-derived peptides and proteins by heterologous expression is the strategy of choice for research groups and pharmaceutical industry to overcome this limitation. Recombinant expression in microorganisms is often the first choice, since bacteria and yeast systems combine high level of recombinant protein expression, fast cell growth and multiplication and simple media requirement. Herein, we present a comprehensive revision, which describes the scorpion venom components that were produced in their recombinant forms using microbial systems. In addition, we highlight the pros and cons of performing the heterologous expression of these compounds, regarding the particularities of each microorganism and how these processes can affect the application of these venom components. The most used microbial system in the heterologous expression of scorpion venom components is Escherichia coli (85%), and among all the recombinant venom components produced, 69% were neurotoxins. This review may light up future researchers in the choice of the best expression system to produce scorpion venom components of interest.

Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice

Diet is an important factor influencing the composition and function of the gut microbiome, but the effect of antimicrobial agents present within foods is currently not understood. In this study, we investigated the effect of the food-grade cationic antimicrobial ε-polylysine on the gut microbiome structure and predicted metagenomic function in a mouse model. The relative abundances of predominant phyla and genera, as well as the overall community structure, were perturbed in response to the incorporation of dietary ε-polylysine. Unexpectedly, this modification to the gut microbiome was experienced transiently and resolved to the initial basal composition at the final sampling point. In addition, a differential non-random assembly was observed in the microbiomes characterized from male and female co-housed animals, although their perturbation trajectories in response to diet remain consistent. In conclusion, antimicrobial ε-polylysine incorporated into food systems transiently alters gut microbial communities in mice, as well as their predicted function. This indicates a dynamic but resilient microbiome that adapts to microbial-active dietary components.

Fermentation parameter optimization of microbial oxalic acid production from cashew apple juice

The potential of cashew apple juice (CAJ) as a carbon source for oxalic acid (OA) production via fermentation process was investigated in this study. The effects and interactions of CAJ concentration, time, pH, NaNO₃ concentration and methanol concentration on OA production were determined in a central composite design (CCD) and the process was modelled and optimized using response surface methodology (RSM). The results showed that OA fermentation can be described significantly (p < 0.05) by a quadratic model giving regression coefficient (R²) of 0.9964. NaNO₃ concentration was the most significant positive variable while methanol was not a significant variable. A maximum OA concentration of 122.68 g/l could be obtained using the optimum levels of CAJ of 150.0 g/l, pH of 5.4, time of 7.31 days, NaNO₃ of 2 g/l and methanol of 1% volume. The production of OA was found to increase from 106.75 to 122.68 g/l using the statistically design optimization. This study revealed that CAJ could serve as an inexpensive and abundant feedstock for fermentative OA production, the resulting model could be used in the design of a typical pilot plant for a scale up production.