Alterations in the Cell Wall of Rhodococcus biphenylivorans Under Norfloxacin Stress

The viable but non-culturable (VBNC) status of Shewanella putrefaciens (S. putrefaciens) with thermosonication (TS) treatment

Although thermosonication (TS) treatment has been widely used in food sterilization, the viable but non-culturable (VBNC) of bacteria with TS treatment has still concerned potential food safety and public health. The molecular mechanism of VBNC status of bacteria with TS treatment is not clearly known. Therefore, in this study, we used Shewanella putrefaciens, which was a common putrefactive bacteria in aquatic products, to study the VBNC state of bacteria with TS treatment. Firstly, our results revealed that S. putrefaciens still could enter the VBNC state after TS treatments: 50 kHz, 300 W, 30 min ultrasonic treatment and 70 °C heating; Subsequently, we found the VBNC state of S. putrefaciens can resist the damage of TS treatment, such as cell wall break, DNA degradation, etc; Finally, four-dimensional data-independent acquisition-based proteomics showed that under VBNC state, S. putrefaciens upregulated functional proteins to resist TS treatment, such as: ribosomal proteins to accelerate the synthesis of stress proteins to counteract TS treatments, ornithine decarboxylase SpeF and MraY to repair TS treatment-induced damage, etc. Meanwhile, S. putrefaciens downregulates metabolic and transport functional proteins such as dehydrogenase to reduce the metabolism. Importantly, among those proteins, the ribosomal transcriptional regulatory protein family, such as rpsB, etc, may be the key proteins for S. putrefaciens entering VBNC state. This finding can provide some new strategies for preventing VBNC status of bacteria with TS treatment, such as: inhibition of key proteins, etc.

Induction and comparative resuscitation of viable but nonculturable state on Vibrio parahaemolyticus serotypes O3:K6 and O1:K25

Vibrio parahaemolyticus, an important food-borne pathogens found to be associated with seafoods and marine environs. It has been a topic of debate for many decades that most pathogens are known to enter a viable but nonculturable (VBNC) state under cold temperature and nutrient limited conditions. The present study examined the time required for the induction of VBNC state and the revival strategies of both the endemic O3:K6 and O1:K25 sporadic strains of V. parahaemolyticus. The results revealed that V. parahaemolyticus survived even after 55 days of incubation in nutrient starved media such as phosphate buffered saline (PBS) and Coastal Water (CW) and could be recovered by temperature upshift method, and compared the resuscitation using Dulbecco's Modified Eagle Medium (DMEM), sheep blood serum, chitin flakes with live Artemia salina, and the results suggests that chitin plays a significant role in regulating the VBNC state. It was also confirmed by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscope (SEM) analysis that VBNC cells can alter their morphology to coccoid forms in order to survive in most extreme nutrient limited environment. Further data on the promoting factors and the exact mechanism that resuscitate VBNC V. parahaemolyticus in cold natural environments and frozen foods are needed to perform a robust risk assessment.

Understanding the transition to viable but non-culturable state in Escherichia coli W3110: a comprehensive analysis of potential spectrochemical biomarkers

The viable but non-culturable (VBNC) state is considered a survival strategy employed by bacteria to endure stressful conditions, allowing them to stay alive. Bacteria in this state remain unnoticed in live cell counts as they cannot proliferate in standard culture media. VBNC cells pose a significant health risk because they retain their virulence and can revive when conditions normalize. Hence, it is crucial to develop fast, reliable, and cost-effective methods to detect bacteria in the VBNC state, particularly in the context of public health, food safety, and microbial control assessments. This research examined the biomolecular changes in Escherichia coli W3110 induced into the VBNC state in artificial seawater under three different stress conditions (temperature, metal, and antibiotic). Initially, confirmation of VBNC cells under various stresses was done using fluorescence microscopy and plate counts. Subsequently, lipid peroxidation was assessed through the TBARS assay, revealing a notable increase in peroxidation end-products in VBNC cells compared to controls. ATR-FTIR spectroscopy and chemomometrics were employed to analyze biomolecular changes, uncovering significant spectral differences in RNA, protein, and nucleic acid concentrations in VBNC cells compared to controls. Notably, RNA levels increased, while protein and nucleic acid amounts decreased. ROC analyses identified the 995 cm- 1 RNA band as a consistent marker across all studied stress conditions, suggesting its potential as a robust biomarker for detecting cells induced into the VBNC state under various stressors.

Emerging contaminants in the water environment: Disinfection-induced viable but non-culturable waterborne pathogens

Disinfection is essential for the control of waterborne pathogens (WPs), especially during the COVID-19 pandemic. WP can enter the viable but non-culturable (VBNC) state to evade disinfection, seriously threatening water safety. VBNC WPs should be considered as an emerging contaminant to ensure a higher level of safety of the water environment. Here, this study systematically reviewed the water disinfection methods that could induce WPs into the VBNC state, and clarified the risks of different species of VBNC WPs in the relevant water environment. The physicochemical and physiological properties of VBNC cells (e.g., morphology, physiology, and resuscitation potential) were then evaluated to better understand their potential health risks. In addition, the dominant detection methods of VBNC WPs were discussed, and real-time and label-free technologies were recommended for the study of VBNC WPs in the aquatic environment. The possible mechanisms of formation and persistence at the genetic level were highlighted. It concluded that the VBNC state has a deeper level of dormancy than the persistent state, which is associated with the general stress response and stringent response systems, and its persistence is also associated with the active efflux of harmful substances. Finally, the current shortcomings and research perspectives of VBNC bacteria were summarized. This review provides new insights into the characteristics, detection methods, persistence mechanisms, and potential health risks of VBNC WPs induced by water disinfection processes, and also serves as a basis for microbial risk control in the aquatic environment.

A synergistic approach combining Adsorption and Biodegradation for effective treatment of Acid Blue 113 dye by Klebsiella grimontii entrapped Graphene Oxide-Calcium Alginate Hydrogel Beads

This study investigated the degradation of Acid Blue 113 (AB 113) dye using Klebsiella grimontii entrapped Graphene Oxide-Calcium Alginate Hydrogel beads (KG-GO-CA) in a Fluidized Bed Bioreactor (FBBR) under varying inlet loading rates. The minimum fluidization velocity of the KG-GO-CA hydrogel beads in FBBR was found to be 0.15 mm/s. The KG-GO-CA beads showed a maximum removal efficiency of 94.6% at an inlet flow rate of 20 mL/h over 15 days. Reusability studies indicated a removal efficiency of 70.6 ± 2.5% for AB 113 after the 12th cycle. Langmuir adsorption isotherm showed the best fit (R2 = 0.98724) with model parameters of Qm (203.83 mg/g) and Ki (0.0101 L/g). The study also confirmed that treated wastewater was more environmentally safe for domestic and commercial uses than untreated wastewater. The research highlights the potential use of KG-GO-CA hydrogel beads for removing dyes from wastewater.

Phenotype and metabolism alterations in PCB-degrading Rhodococcus biphenylivorans TG9T under acid stress

Environmental acidification impairs microorganism diversity and their functions on substance transformation. Rhodococcus is a ubiquitously distributed genus for contaminant detoxification in the environment, and it can also adapt a certain range of pH. This work interpreted the acid responses from both phenotype and metabolism in strain Rhodococcus biphenylivorans TG9^T (TG9) induced at pH 3. The phenotype alterations were described with the number of culturable and viable cells, intracellular ATP concentrations, cell shape and entocyte, degradation efficiency of polychlorinated biphenyl (PCB) 31 and biphenyl. The number of culturable cells maintained rather stable within the first 10 days, even though the other phenotypes had noticeable alterations, indicating that TG9 possesses certain capacities to survive under acid stress. The metabolism responses were interpreted based on transcription analyses with four treatments including log phase (LP), acid-induced (PER), early recovery after removing acid (RE) and later recovery (REL). With the overview on the expression regulations among the 4 treatments, the RE sample presented more upregulated and less downregulated genes, suggesting that its metabolism was somehow more active after recovering from acid stress. In addition, the response mechanism was interpreted on 10 individual metabolism pathways mainly covering protein modification, antioxidation, antipermeability, H⁺ consumption, neutralization and extrusion. Furthermore, the transcription variations were verified with RT-qPCR on 8 genes with 24-hr, 48-hr and 72-hr acid treatment. Taken together, TG9 possesses comprehensive metabolism strategies defending against acid stress. Consequently, a model was built to provide an integrate insight to understand the acid resistance/tolerance metabolisms in microorganisms.

Extended lag phase indicates the dormancy of biphenyl degrading Rhodococcus biphenylivorans TG9 under heat stress

Microbial remediation is a green and sustainable technology, but harsh environmental conditions could lead to microbial dormancy, such as entering a viable but non-culturable (VBNC) state. However, the evidence of VBNC is controversial and limited. In this study, heat stress (60 °C), one of the leading challenges for mesophilic degrading bacteria, was mimicked to investigate the physiological response of Rhodococcus biphenylivorans TG9. After 2 h of heat stress, the culturable TG9 cell count decreased from 10⁸ cells/mL to undetectable while the viable cell count was still 10⁵ cells/mL. The biphenyl degradation efficiency of stressed TG9 dropped by 50% compared to that of cells at logarithmic phase. During heat stress, the respiratory activity of TG9 declined dramatically while the intracellular ATP level initially increased and then decreased. Notably, the corresponding indicators recovered when restored to 30 °C. These characteristics were in consistent with bacteria entering into VBNC state. Furthermore, fluorescence activated cell sorting together with single cell as seed culture detection verified the unculturability and viability of VBNC state of TG9 cells. Also, we found that single cells in VBNC state could resuscitate and regrowth with significantly extended lag phase (LP). Our results highlight the potential of TG9 for microbial remediation and hint LP duration as an indicator for survival state of bacteria.

Enzymatic properties and biological activity of resuscitation-promoting factor B of Rhodococcus sp. (GX12401)

Resuscitation-promoting factor B (RpfB) is one of the five members of Rpf-like family in Mycobacteriales, which have the resuscitation-promoting activity. Most strains of Rhodococcus also have RpfB gene, but the study of rpfB gene in Rhodococcus is not thorough. Here, we amplified the rpfB gene of intact Rhodococcus sp. (GX12401) and cloned it into pET30a (+) expression vector. Then a recombinant form of soluble RpfB was expressed in Escherichia coli BL21. The soluble recombinant RpfB was purified by Ni–Sepharose affinity chromatography and molecular weight of the protein was 55 kDa, determined by 12% SDS–PAGE stained with Coomassie brilliant blue R-250. When 4-methylumbelliferyl-β-D-N,N′,N″-triacetylchitoside was used as enzyme substrate to test lysozyme activity, the recombinant protein RpfB had good stability and enzyme activity, and the lysozyme activity was low (4.74 U), among which Mg²⁺, Na⁺, Al³⁺ and DMSO could significantly increase the activity of RpfB. The purified recombinant protein was added to Rhodococcus VBNC cells, and the VBNC cells were resuscitated at the concentration of 1 picomolar concentrations, which increased by 18% compared with the control, while the cell resuscitation was inhibited at the concentration of 1,000 picomolar concentrations. Therefore, RpfB can improve the survival ability of Rhodococcus in extreme or harsh environment and enhance the corresponding biological activity.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Antibiotic tolerance and degradation capacity of the organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9T

Antibiotics are ubiquitous in soil due to natural ecological competition, as well as emerging contaminants due to anthropogenic inputs. Under environmental factors like antibiotic stress, some bacteria, including those that degrade environmental pollutants, can enter a dormant state as a survival strategy, thereby limiting their metabolic activity and function. Dormancy has a critical influence on the degradative activity of bacteria, dramatically decreasing the rate at which they transform organic pollutants. To better understand this phenomenon in environmental pollutant-degrading bacteria, we investigated dormancy transitions induced with norfloxacin in Rhodococcus biphenylivorans TG9^T using next-generation proteomics, proteogenomics, and additional experiments. Our results suggest that exposure to norfloxacin inhibited DNA replication, which led to damage to the cell. Dormant cells then likely triggered DNA repair, particularly homologous recombination, for continued survival. The results also indicated that substrate transport (ATP-binding cassette transporter), ATP production, and the tricarboxylic acid (TCA) cycle were repressed during dormancy, and degradation of organic pollutants was down-regulated. Given the widespread phenomenon of dormancy among bacteria involved in pollutant removal systems, this study improves our understanding of possible implications of antibiotic survival strategies on biotransformation of mixtures containing antibiotics as well as other organics.

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model

BACKGROUND

Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear.

RESULTS

By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes.

CONCLUSIONS

This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.