Identification, characterization and molecular analysis of the viable but nonculturable Rhodococcus biphenylivorans

Autocrine peptides inhibited the formation of VBNC state of Staphylococcus aureus

Viable but non-culturable (VBNC) Staphylococcus aureus cannot form colonies on a medium, causing a false negative result in culture-based detection, which is a potential hazard to human health. In this study, four peptides (PVSS.a-1, PVSS.a-2, PVSS.a-3, and PVSS.a-4) were identified in the suspension of S. aureus during the VBNC state induction. Notably, PVSS.a-1 and PVSS.a-2 prolonged the entry of S. aureus into the VBNC state in citric acid solution (pH 4.0) at 4℃ by 83 % and 103 %, respectively. Such a delaying effect indicates that S. aureus might be forced to enter the VBNC state under pressure, rather than actively. Microscopic observation and zeta-potential determination suggested that PVSS.a-1 and PVSS.a-2 improved the aggregation of S. aureus cells. Furthermore, the two peptides were demonstrated to enter cells by FITC-label localization detection, and changed internal structures and improved intracellular enzyme activities occurred in the two peptide-treated cells. Through the analysis of interactions with DNA and proteins of S. aureus, it was found that PVSS.a-1 and PVSS.a-2 might affect cellular processes, including cell division, transcription, translation, and material and energy metabolisms. These alterations improved the viability and culturability of S. aureus, thereby delaying VBNC formation. In summary, our study reveals how autocrine peptides delay VBNC formation of S. aureus, and provides a new insight into the real intention of bacteria to form VBNC state under adverse conditions.

Enhanced dechlorination and degradation of Aroclor 1260 by resuscitation-promoting factor under alternating anaerobic-aerobic conditions: Superior performance and associated microbial populations

The combined processes of dechlorination and degradation are essential for the effective bioremediation of environments contaminated with complex polychlorinated biphenyl (PCB) mixtures. Although resuscitation-promoting factor (Rpf) has been reported to enhance anaerobic dechlorination and aerobic degradation of PCBs by microorganisms, its impact on microbial populations during alternating anaerobic-aerobic treatments remains unexplored. This study investigated the dechlorination and degradation of Aroclor 1260 under anaerobic (AN), aerobic (AE), and alternating anaerobic-aerobic (AA) conditions, both with and without Rpf supplementation. The results demonstrated that Rpf significantly promoted Aroclor 1260 dechlorination under AN conditions, enhanced degradation under AE conditions, and markedly improved both processes under AA conditions, achieving nearly twice the degradation efficiency compared to AE alone. Furthermore, Rpf supplementation significantly increased the abundance of dechlorination-associated microbial taxa, including members of Firmicutes, Chloroflexi, Bacteroidota, and Desulfobacterota under AN conditions, as well as degradation-associated genera such as Pseudomonas and Sphingomonas under AE and AA conditions. Rpf also strengthened microbial interactions by enhancing positive correlations among functional populations and increasing network complexity. These findings establish Rpf as a powerful enhancer of PCB dechlorination and degradation, which provide valuable insights into its superior efficiency in PCB removal under AA conditions.

Formation and resuscitation of viable but non-culturable (VBNC) yeast in the food industry: A review

The viable but non-culturable (VBNC) state is a survival strategy adopted by microorganisms in response to unfavorable conditions in the environment. VBNC cells are unable to form colonies but still maintain a low level of activity, posing a potential threat to food safety and public health. Therefore, the development of effective strategies to prevent the formation and resuscitation of VBNC cells of microorganisms is a key challenge in food science and microbiology research. However, current research on VBNC cells has primarily focused on bacteria, with relatively limited reports on fungi. This paper provides a comprehensive and systematic review of yeast in the VBNC state, discussing various factors that induce and facilitate resuscitation, along with detection methods and formation and recovery mechanisms. A comprehensive understanding of the induction and resuscitation of yeast in the VBNC state and exploration of its molecular mechanism hold significant implications for food safety and public health. It is imperative to enhance our comprehension of the underlying mechanisms and contributory factors pertaining to VBNC yeast, thereby facilitating the efficient management of the food fermentation process and ensuring the integrity of food quality and safety.

Enhanced microbial dechlorination of PCBs by anaerobic digested sludge and enrichment of low-abundance PCB dechlorinators

The slow rate of anaerobic microbial dechlorination in natural environments limits the application of polychlorinated biphenyl (PCB) bioremediation. Anaerobic digested sludge (ADS), abundant in nutrients and microorganisms, could be an effective additive to improve microbial dechlorination. This research investigates the influence of ADS on Aroclor 1260 dechlorination performance, microbial community composition, and the abundance of functional genes. Moreover, further enrichment of organohalide-respiring bacteria (OHRB) was examined using tetrachloroethene (PCE) as the electron acceptor, followed by the serial dilution-to-extinction method in conjunction with resuscitation promoting factor (Rpf) supplementation. The results demonstrated that the addition of 5 g/L ADS achieved more extensive and efficient dechlorination of PCBs. ADS enhanced the removal of meta- and para-chlorine without significantly changing the dechlorination pathways. The abundances of dechlorinators, including Dehalobium and Dehalobacter within the Chloroflexi and Firmicutes phyla, as well as non-dechlorinators from the Desulfobacterota, Euryarchaeota, and Bacteroidetes phyla, were significantly increased with ADS amendment. Similarly, an increased abundance of bacteria, OHRB, reductive dehalogenase (RDase) genes, and archaeal 16S rRNA genes was observed. Additionally, obligate OHRB, such as Dehalobacter and Dehalobium, were further enriched. These findings indicate that ADS effectively enhances microbial reductive dechlorination and highlight the potential for enriching and isolating OHRB with Rpf.

Enhanced biodegradation of polychlorinated biphenyls by co-cultivation of resuscitated strains with unique advantages

The investigation into viable but non-culturable (VBNC) bacteria through the implementation of resuscitation promoting factors (Rpfs) has broadened the potential sources for isolating strains capable of degrading polychlorinated biphenyls (PCBs). Nonetheless, there has been limited research on the efficacy of resuscitated strains and the potential improvement of their performance through co-cultivation. In this work, the PCB degradation potential of resuscitated strains, specifically Pseudomonas sp. HR1 and Achromobacter sp. HR2, as well as their co-cultures, was investigated. Of particular importance was the comparative analysis between the optimal co-culture and individual strains regarding their ability to degrade PCB homologs and mineralize intermediate metabolites. The results suggested that the resuscitated strains HR1 and HR2 demonstrated robust growth and effective degradation of Aroclor 1242. The co-culture CO13, with an optimal HR1 to HR2 ratio of 1:3, exhibited a remarkable improvement in PCB degradation and intermediate metabolite mineralization compared to individual strains. Analysis of functional genes and degradation metabolites revealed that both the individual strains and co-culture CO13 degraded PCBs via the HOPDA-benzoate pathway, then mineralized through protocatechuate meta- and ortho-cleavage pathways, as well as the catechol ortho-cleavage pathway. This study represents the first documentation of the improved PCB degradation through the co-cultivation of resuscitated strains, which highlights the great promise of these resuscitated strains and their co-cultures as effective bio-inoculants for enhanced bioremediation.

Legionella colonization and 3D spatial location within a Pseudomonas biofilm

Biofilms are known to be critical for Legionella settlement in engineered water systems and are often associated with Legionnaire's Disease events. One of the key features of biofilms is their heterogeneous three-dimensional structure which supports the establishment of microbial interactions and confers protection to microorganisms. This work addresses the impact of Legionella pneumophila colonization of a Pseudomonas fluorescens biofilm, as information about the interactions between Legionella and biofilm structures is scarce. It combines a set of meso- and microscale biofilm analyses (Optical Coherence Tomography, Episcopic Differential Interference Contrast coupled with Epifluorescence Microscopy and Confocal Laser Scanning Microscopy) with PNA-FISH labelled L. pneumophila to tackle the following questions: (a) does the biofilm structure change upon L. pneumophila biofilm colonization?; (b) what happens to L. pneumophila within the biofilm over time and (c) where is L. pneumophila preferentially located within the biofilm? Results showed that P. fluorescens structure did not significantly change upon L. pneumophila colonization, indicating the competitive advantage of the first colonizer. Imaging of PNA-labelled L. pneumophila showed that compared to standard culture recovery it colonized to a greater extent the 3-day-old P. fluorescens biofilms, presumably entering in VBNC state by the end of the experiment. L. pneumophila was mostly located in the bottom regions of the biofilm, which is consistent with the physiological requirements of both bacteria and confers enhanced Legionella protection against external aggressions. The present study provides an expedited methodological approach to address specific systematic laboratory studies concerning the interactions between L. pneumophila and biofilm structure that can provide, in the future, insights for public health Legionella management of water systems.

Study on the estradiol degradation gene expression and resistance mechanism of Rhodococcus R-001 under low-temperature stress

Estradiol (E2), an endocrine disruptor, acts by mimicking or interfering with the normal physiological functions of natural hormones within organisms, leading to issues such as endocrine system disruption. Notably, seasonal fluctuations in environmental temperature may influence the degradation speed of estradiol (E2) in the natural environment, intensifying its potential health and ecological risks. Therefore, this study aims to explore how bacteria can degrade E2 under low-temperature conditions, unveiling their resistance mechanisms, with the goal of developing new strategies to mitigate the threat of E2 to health and ecological safety. In this paper, we found that Rhodococcus equi DSSKP-R-001 (R-001) can efficiently degrade E2 at 30 °C and 10 °C. Six genes in R-001 were shown to be involved in E2 degradation by heterologous expression at 30 °C. Among them, 17β-HSD, KstD2, and KstD3, were also involved in E2 degradation at 10 °C; KstD was not previously known to degrade E2. RNA-seq was used to characterize differentially expressed genes (DEGs) to explore the stress response of R-001 to low-temperature environments to elucidate the strain's adaptation mechanism. At the low temperature, R-001 cells changed from a round spherical shape to a long rod or irregular shape with elevated unsaturated fatty acids and were consistent with the corresponding genetic changes. Many differentially expressed genes linked to the cold stress response were observed. R-001 was found to upregulate genes encoding cold shock proteins, fatty acid metabolism proteins, the ABC transport system, DNA damage repair, energy metabolism and transcriptional regulators. In this study, we demonstrated six E2 degradation genes in R-001 and found for the first time that E2 degradation genes have different expression characteristics at 30 °C and 10 °C. Linking R-001 to cold acclimation provides new insights and a mechanistic basis for the simultaneous degradation of E2 under cold stress in Rhodococcus adaptation.

Echinocandin persistence directly impacts the evolution of resistance and survival of the pathogenic fungus Candida glabrata

Recent epidemiological studies documented an alarming increase in the prevalence of echinocandin-resistant (ECR) Candida glabrata blood isolates. ECR isolates are known to arise from a minor subpopulation of a clonal population, termed echinocandin persisters. Although it is believed that isolates with a higher echinocandin persistence (ECP) are more likely to develop ECR, the implication of ECP needs to be better understood. Moreover, replacing laborious and time-consuming traditional approaches to determine ECP levels with rapid, convenient, and reliable tools is imperative to advance our understanding of this emerging concept in clinical practice. Herein, using extensive ex vivo and in vivo systemic infection models, we showed that high ECP isolates are less effectively cleared by micafungin treatment and exclusively give rise to ECR colonies. Additionally, we developed a flow cytometry-based tool that takes advantage of a SYTOX-based assay for the stratification of ECP levels. Once challenged with various collections of echinocandin-susceptible blood isolates, our assay reliably differentiated ECP levels in vitro and predicted ECP levels in real time under ex vivo and in vivo conditions when compared to traditional methods relying on colony-forming unit counting. Given the high and low ECP predictive values of 92.3% and 82.3%, respectively, our assay showed a high agreement with traditional approach. Collectively, our study supports the concept of ECP level determination in clinical settings and provides a robust tool scalable for high-throughput settings. Application of this tool facilitates the interrogation of mutant and drug libraries to further our understanding of persister biology and designing anti-persister therapeutics.

IMPORTANCE

Candida glabrata is a prevalent fungal pathogen able to replicate inside macrophages and rapidly develop resistance against frontline antifungal echinocandins. Multiple studies have shown that echinocandin resistance is fueled by the survival of a small subpopulation of susceptible cells surviving lethal concentrations of echinocandins. Importantly, bacterial pathogens that exhibit high antibiotic persistence also impose a high burden and generate more antibiotic-resistant colonies. Nonetheless, the implications of echinocandin persistence (ECP) among the clinical isolates of C. glabrata have not been defined. Additionally, ECP level determination relies on a laborious and time-consuming method, which is prone to high variation. By exploiting in vivo systemic infection and ex vivo models, we showed that C. glabrata isolates with a higher ECP are associated with a higher burden and more likely develop echinocandin resistance upon micafungin treatment. Additionally, we developed an assay that reliably determines ECP levels in real time. Therefore, our study identified C. glabrata isolates displaying high ECP levels as important entities and provided a reliable and convenient tool for measuring echinocandin persistence, which is extendable to other fungal and bacterial pathogens.

Unveiling the distribution characteristics of rpf-like genes and indigenous resuscitation promoting factor production in PCB-contaminated soils

Resuscitation promoting factors (Rpfs), known for their anti-dormancy cytokine properties, have been extensively investigated in the medical field. Although the Rpf from Micrococcus luteus has been successfully utilized to resuscitate and stimulate microbial populations for the degradation of polychlorinated biphenyls (PCBs), the presence of indigenous Rpf homologs in PCB-contaminated soils has not been established. In this study, the distribution characteristics of rpf-like genes and indigenous strain capable of producing Rpf in PCB-contaminated soils were explored. The results revealed the widespread presence of Rpf-like domains and their associated genes, particularly in close association with heavy metals and PCBs. The rpf-like genes were predominantly found in Proteobacteria and displayed a positive correlation with genes involved in PCB degradation and viable but non-culturable (VBNC) formation. Notably, the recombinant Rpf-Ac protein derived from the indigenous strain Achromobacter sp. HR2 exhibited muralytic activity and demonstrated significant efficacy in resuscitating the growth of VBNC cells, while also stimulating the growth of normal cells. These findings shed light on the prevalent presence of Rpf homologs in PCB-contaminated soils and their potential to resuscitate functional populations in the VBNC state, thereby enhancing in situ bioremediation.

New insights into survival strategies and PCB bioremediation potential of resuscitated strain Achromobacter sp. HR2 under combined stress conditions

The resuscitated strains achieved through the addition of resuscitation promoting factor (Rpf) hold significant promise as bio-inoculants for enhancing the bioremediation of polychlorinated biphenyls (PCBs). Nevertheless, the potential of these resuscitated strains to transition into a viable but non-culturable (VBNC) state, along with the specific stressors that initiate this transformation, remains to be comprehensively elucidated. In this study, a resuscitated strain HR2, obtained through Rpf amendment, was employed to investigate its survival strategies under combined stress involving low temperature (LT), and PCBs, in the absence and presence of heavy metals (HMs). Whole-genome analysis demonstrated that HR2, affiliated with Achromobacter, possessed 107 genes associated with the degradation of polycyclic aromatic compounds. Remarkably, HR2 exhibited effective degradation of Aroclor 1242 and robust resistance to stress induced by LT and PCBs, while maintaining its culturability. However, when exposed to the combined stress of LT, PCBs, and HMs, HR2 entered the VBNC state. This state was characterized by significant decreases in enzyme activities and notable morphological, physiological, and molecular alterations compared to normal cells. These findings uncovered the survival status of resuscitated strains under stressful conditions, thereby offering valuable insights for the development of effective bioremediation strategies.

Unveiling the PCB biodegradation potential and stress survival strategies of resuscitated strain Pseudomonas sp. HR1

The exploration of resuscitated strains, facilitated by the resuscitation promoting factor (Rpf), has substantially expanded the pool of cultivated degraders, enhancing the screening of bio-inoculants for bioremediation applications. However, it remains unknown whether these resuscitated strains can re-enter the viable but non-culturable (VBNC) state and the specific stress conditions that trigger such a transition. In this work, the whole genome, and polychlorinated biphenyl (PCB)-degrading capabilities of a resuscitated strain HR1, were investigated. Notably, the focus of this exploration was on elucidating whether HR1 would undergo a transition into the VBNC state when exposed to low temperature and PCBs, with and without the presence of heavy metals (HMs). The results suggested that the resuscitated strain Pseudomonas sp. HR1 harbored various functional genes related to xenobiotic biodegradation, demonstrating remarkable efficiency in Aroclor 1242 degradation and strong resistance against stress induced by low temperature and PCBs. Nevertheless, when exposed to the combined stress of low temperature, PCBs, and HMs, HR1 underwent a transition into the VBNC state. This transition was characterized by significant decreases in enzyme activities and notable changes in both morphological and physiological traits when compared to normal cells. Gene expression analysis revealed molecular shifts underlying the VBNC state, with down-regulated genes showed differential expression across multiple pathways and functions, including oxidative phosphorylation, glycolysis, tricarboxylic acid cycle, amino acid metabolism, translation and cytoplasm, while up-regulated genes predominantly associated with transcription regulation, membrane function, quorum sensing, and transporter activity. These findings highlighted the great potential of resuscitated strains as bio-inoculants in bioaugmentation and shed light on the survival mechanisms of functional strains under stressful conditions, which should be carefully considered during bioremediation processes.

Plasma-generated nitric oxide water: A promising strategy to combat bacterial dormancy (VBNC state) in environmental contaminant Micrococcus luteus

The viable but non-culturable (VBNC) is an inactive state, and certain bacteria can enter under adverse conditions. The VBNC state challenges the environment, food safety, and public health since VBNCs may resuscitate and pose a risk to human health. The aim of this study was to investigate the effect of plasma-generated nitric oxide water (PG-NOW) on airborne contaminant Micrococcus luteus (M. luteus) and examine its potential to induce the VBNC state. The essential conditions for bacteria to enter VBNC state are low metabolic activity and rare or no culturable counts. The results indicated that PG-NOW effectively eliminates M. luteus, and the remaining bacteria are in culturable condition. Moreover, the conventional cultured-based method combined with a propidium iodide monoazide quantitative PCR (PMAxxTM-qPCR) showed no significant VBNC induction and moderate culturable counts. Results from the qPCR revealed that gene levels in PG-NOW treated bacteria related to resuscitation-promoting factors, amino acid biosynthesis, and fatty acid metabolism were notably upregulated. PG-NOW inactivated M. luteus showed negligible VBNC formation and alleviated infection ability in lung cells. This study provides new insights into the potential use of PG-NOW reactive species for the prevention and control of the VBNC state of M. luteus.

Quantitative Proteomic Analysis on the Slightly Acidic Electrolyzed Water Triggered Viable but Non-Culturable Listeria monocytogenes

This study undertakes a comprehensive exploration of the impact of slightly acidic electrolyzed water (SAEW) on Listeria monocytogenes, a common foodborne pathogen, with a particular focus on understanding the molecular mechanisms leading to the viable but nonculturable (VBNC) state. Given the widespread application of SAEW as an effective disinfectant in the food industry, uncovering these molecular pathways is crucial for improving food safety measures. We employed tandem mass tags (TMT), labeling proteomic techniques and LC-MS/MS to identify differentially expressed proteins under two doses of SAEW conditions. We indicated 203 differential expressed proteins (DEPs), including 78 up-regulated and 125 down-regulated DEPs. The functional enrichment analysis of these proteins indicated that ribosomes, biosynthesis of secondary metabolites, and aminoacyl-tRNA biosynthesis were enriched functions affected by SAEW. Further, we delved into the role of protein chlorination, a potential consequence of reactive chlorine species generated during the SAEW production process, by identifying 31 chlorinated peptides from 22 proteins, with a dominant sequence motif of Rxxxxx[cY] and functionally enriched in translation. Our findings suggest that SAEW might prompt alterations in the protein translation process and trigger compensatory ribosome biosynthesis. However, an imbalance in the levels of elongation factors and AARSs could hinder recovery, leading to the VBNC state. This research carries substantial implications for food safety and sanitation, as it adds to our understanding of the SAEW-induced VBNC state in L. monocytogenes and offers potential strategies for its control.

Citral and trans-cinnamaldehyde, two plant-derived antimicrobial agents can induce Staphylococcus aureus into VBNC state with different characteristics

Viable but nonculturable (VBNC) state bacteria are difficult to detect in the food industry due to their nonculturable nature and their recovery characteristics pose a potential threat to human health. The results of this study indicated that S. aureus was found to enter the VBNC state completely after induced by citral (1 and 2 mg/mL) for 2 h, and after induced by trans-cinnamaldehyde (0.5 and 1 mg/mL) for 1 h and 3 h, respectively. Except for VBNC state cells induced by 2 mg/mL citral, the VBNC state cells induced by the other three conditions (1 mg/mL citral, 0.5 and 1 mg/mL trans-cinnamaldehyde) were able to be resuscitated in TSB media. In the VBNC state cells induced by citral and trans-cinnamaldehyde, the ATP concentration was reduced, the hemolysin-producing ability was significantly decreased, but the intracellular ROS level was elevated. The results of heat and simulated gastric fluid experiments showed different environment resistance on VBNC state cells induced by citral and trans-cinnamaldehyde. In addition, by observing the VBNC state cells showed that irregular folds on the surface, increased electron density inside and vacuoles in the nuclear region. What's more, S. aureus was found to enter the VBNC state completely after induced by meat-based broth containing citral (1 and 2 mg/mL) for 7 h and 5 h, after induced by meat-based broth containing trans-cinnamaldehyde (0.5 and 1 mg/mL) for 8 h and 7 h. In summary, citral and trans-cinnamaldehyde can induce S. aureus into VBNC state and food industry needs to comprehensively evaluate the antibacterial capacity of these two plant-derived antimicrobial agents.

Resuscitation-Promoting Factor Accelerates Enrichment of Highly Active Tetrachloroethene/Polychlorinated Biphenyl-Dechlorinating Cultures

The anaerobic bioremediation of polychlorinated biphenyls (PCBs) is largely impeded by difficulties in massively enriching PCB dechlorinators in short periods of time. Tetrachloroethene (PCE) is often utilized as an alternative electron acceptor to preenrich PCB-dechlorinating bacteria. In this study, resuscitation promoting factor (Rpf) was used as an additive to enhance the enrichment of the microbial communities involved in PCE/PCBs dechlorination. The results indicated that Rpf accelerates PCE dechlorination 3.8 to 5.4 times faster than control cultures. In Aroclor 1260-fed cultures, the amendment of Rpf enables significantly more rapid and extensive dechlorination of PCBs. The residual high-chlorinated PCB congeners (≥5 Cl atoms) accounted for 36.7% and 59.8% in the Rpf-amended cultures and in the corresponding controls, respectively. This improvement was mainly attributed to the enhanced activity of the removal of meta-chlorines (47.7 mol % versus 14.7 mol %), which did not appear to affect dechlorination pathways. The dechlorinators, including Dehalococcoides in Chloroflexi and Desulfitobacterium in Firmicutes, were greatly enriched via Rpf amendment. The abundance of nondechlorinating populations, including Methanosarcina, Desulfovibrio, and Bacteroides, was also greatly enhanced via Rpf amendment. These results suggest that Rpf serves as an effective additive for the rapid enrichment of active dechlorinating cultures so as to provide a new approach by which to massively cultivate bioinoculants for accelerated in situ anaerobic bioremediation. IMPORTANCE The resuscitation promoting factor (Rpf) of Micrococcus luteus has been reported to resuscitate and stimulate the growth of functional microorganisms that are involved in the aerobic degradation of polychlorinated biphenyls (PCBs). However, few studies have been conducted to investigate the role of Rpf on anaerobic microbial populations. In this study, the enhancement of Rpf on the anaerobic microbial dechlorination of PCE/PCBs was discovered. Additionally, the Rpf-responsive populations underlying the enhanced dechlorination were uncovered. This report reveals the rapid enrichment of active dechlorinating cultures via Rpf amendment, and this sheds light on massively enriching PCB dechlorinators in short periods of time. The enhanced in situ anaerobic bioremediation of PCBs could be expected by supplementing Rpf.

High PCBs mineralization capability of a resuscitated strain Bacillus sp. LS1 and its survival in PCB-contaminated soil

Polychlorinated biphenyl (PCB)-degrading strains resuscitated by resuscitation promoting factor (Rpf) enlarged pure degraders to screen effective bio-inoculants for soil bioaugmentation. In this study, whole-genome analysis and PCB-degrading performance of a resuscitated strain LS1 were investigated. Importantly, the persistence and the physiological response of soil-inoculated LS1 were checked. The results indicate that the Bacillus sp. strain LS1 possessed the potential to degrade polycyclic aromatic compounds. LS1 exhibited better performance in degrading PCBs 18 and 52, but lower PCB 77 degradation capability. At PCBs concentration of 10 mg/L, the degradation efficiencies of PCBs 18, 52 and 77 within 96 h were 62.8 %, 59.6 % and 39.8 %, respectively. Combined the bph genes and metabolites detected, as well as the genes found in the genome, the abilities of LS1 for oxidative dehalogenation and mineralization of PCBs via HOPDA-benzoate-protocatechuate-β-ketoadipate pathway were determined. Notably, LS1 can still maintain survival and culturable state after inoculation into PCB-contaminated soil for 70 days. This is the first report to demonstrate the fate of resuscitated strain when used as soil bio-inoculant, which revealed the necessity and feasibility of using resuscitated strains to enhance bioremediation of PCB-contaminated soils.

Wake Up! Resuscitation of Viable but Nonculturable Bacteria: Mechanism and Potential Application

The viable but nonculturable (VBNC) state is a survival strategy for bacteria when encountered with unfavorable conditions. Under favorable environments such as nutrient supplementation, external stress elimination, or supplementation with resuscitation-promoting substances, bacteria will recover from the VBNC state, which is termed "resuscitation". The resuscitation phenomenon is necessary for proof of VBNC existence, which has been confirmed in different ways to exclude the possibility of culturable-cell regrowth. The resuscitation of VBNC cells has been widely studied for the purpose of risk control of recovered pathogenic or spoilage bacteria. From another aspect, the resuscitation of functional bacteria can also be considered a promising field to explore. To support this point, the resuscitation mechanisms were comprehensively reviewed, which could provide the theoretical foundations for the application of resuscitated VBNC cells. In addition, the proposed applications, as well as the prospects for further applications of resuscitated VBNC bacteria in the food industry are discussed in this review.

Ralstonia solanacearum Facing Spread-Determining Climatic Temperatures, Sustained Starvation, and Naturally Induced Resuscitation of Viable but Non-Culturable Cells in Environmental Water

Ralstonia solanacearum is a bacterial phytopathogen affecting staple crops, originally from tropical and subtropical areas, whose ability to survive in temperate environments is of concern under global warming. In this study, two R. solanacearum strains from either cold or warm habitats were stressed by simultaneous exposure to natural oligotrophy at low (4 °C), temperate (14 °C), or warm (24 °C) temperatures in environmental water. At 4 °C, the effect of temperature was higher than that of oligotrophy, since R. solanacearum went into a viable but non-culturable (VBNC) state, which proved to be dependent on water nutrient contents. Resuscitation was demonstrated in vitro and in planta. At 14 °C and 24 °C, the effect of oligotrophy was higher than that of temperature on R. solanacearum populations, displaying starvation-survival responses and morphological changes which were stronger at 24 °C. In tomato plants, starved, cold-induced VBNC, and/or resuscitated cells maintained virulence. The strains behaved similarly regardless of their cold or warm areas of origin. This work firstly describes the natural nutrient availability of environmental water favoring R. solanacearum survival, adaptations, and resuscitation in conditions that can be found in natural settings. These findings will contribute to anticipate the ability of R. solanacearum to spread, establish, and induce disease in new geographical and climatic areas.

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

Overview of VBNC, a survival strategy for microorganisms

Microorganisms are exposed to a wide variety of stress factors in their natural environments. Under that stressful conditions, they move into a viable but nonculturable (VBNC) state to survive and maintain the vitality. At VBNC state, microorganisms cannot be detected by traditional laboratory methods, but they can be revived under appropriate conditions. Therefore, VBNC organisms cause serious food safety and public health problems. To date, it has been determined that more than 100 microorganism species have entered the VBNC state through many chemical and physical factors. During the last four decades, dating from the initial detection of the VBNC condition, new approaches have been developed for the induction, detection, molecular mechanisms, and resuscitation of VBNC cells. This review evaluates the current data of recent years on the inducing conditions and detection methods of the VBNC state, including with microorganisms on the VBNC state, their virulence, pathogenicity, and molecular mechanisms.

Transcriptome analysis and prediction of the metabolic state of stress-induced viable but non-culturable Bacillus subtilis cells

Many bacteria adapt their physiology and enter the viable but non-culturable state to survive prolonged exposure to adverse environmental conditions. The VBNC cells maintain active metabolism, membrane integrity and gene transcription. However, they lose the ability to form colonies on a conventional culture media. Thus, standard colony counting methods cannot detect these alive but dormant cells. The Gram-positive bacterium Bacillus subtilis was found to enter the VBNC state when pre-exposed to osmotic stress and treated with a lethal dose of kanamycin. These cells reduced their metabolic activity, ceased growth and division and became kanamycin-tolerant. Interestingly, despite active metabolism, the majority of the kanamycin tolerant cells could not be revived on LB agar. In this study, we use a robust RNA-Seq technique to elucidate the differences in transcriptional profiles of B. subtilis VBNC cells. A comparative analysis of differently expressed genes and operons performed in this study indicates high similarities in transcriptional responses of VBNC and kanamycin-sensitive cells to antibiotic treatment. Moreover, this work reveals that VBNC cells strongly upregulate genes involved in proline uptake and catabolism, suggesting a putative role of proline as nutrient in VBNC cells.

Impact of temperature, soil type and compost amendment on the survival, growth and persistence of Listeria monocytogenes of non-environmental (food-source associated) origin in soil

Listeria monocytogenes of varied sources including food-related sources may reach the soil. Associated food safety and environmental health risks of such contamination depend significantly on the capacity of L. monocytogenes to survive in the soil. This study assessed the survival of 13 L. monocytogenes strains isolated from food and food processing environments and a cocktail of three of the strains in two types of soils (loam and sandy) under controlled temperature conditions: 5, 10, 20, 25, 30℃ and 'uncontrolled' ambient temperature conditions in a tropical region. The impact of compost amendment on the survival of L. monocytogenes in the two different types of soils was also assessed. Soil type, temperature and compost amendment significantly (P <0.001) impacted the survival of L. monocytogenes in soil. Temperature variations affected the survival of L. monocytogenes in soil, where some strains such as strain 732, a L. monocytogenes 1/2a strain survived better at lower temperature (5°C), for which counts of up to 10.47 ± 0.005 log CFU/g were recovered in compost-amended sandy soil, 60 days post-inoculation. Some other strains such as strain 441, a L. monocytogenes 1/2a survived best at intermediate temperature (25 and 30 °C), while others such as 2739 (L. monocytogenes 1/2b) thrived at higher temperature (between 30 °C - 37 °C). There were significant correlations between the influence of temperature and soil type, where lower temperature conditions (5°C - 20°C) were generally more suitable for survival in sandy soil compared to higher temperature conditions. For some of the strains that thrived better in sandy soil at lower temperature, Pearson correlation analysis found significant correlations between temperature and soil type. Steady, controlled temperature generally favored the survival of the strains compared to uncontrolled ambient temperature conditions, except for the cocktail. The cocktail persisted until the last day of post-inoculation storage (60th day) in all test soils and under all incubation temperature conditions. Loam soil was more favorable for the survival of L. monocytogenes and compost amendment improved the survival of the strains, especially in compost-amended sandy soil. Listeria monocytogenes may exhibit variable survival capacity in soil, depending on conditions such as soil type, compost amendment and temperature.

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.

Pseudomonas fluorescens Cells' Recovery after Exposure to BAC and DBNPA Biocides

A proper assessment of the effects of biocides on bacterial cells is key to the prevention of antimicrobial resistance and the implementation of suitable biocidal programmes. It is particularly relevant regarding the ability of dead-labelled cells to recover their functional processes once the biocide is removed. In the present work, we studied how Pseudomonas fluorescens cells previously exposed to different concentrations of BAC (benzalkonium chloride) and DBNPA (2,2-Dibromo-3-nitrilopropionamide) behave upon the restoration of optimum growth conditions. The following indicators were evaluated: culturability, membrane integrity, metabolic activity (resazurin), cellular energy (ATP), and cell structure and morphology (transmission electron microscopy (TEM)). The results demonstrated that cells previously labelled as 'dead' recovered to a greater extent in all indicators. Only cells previously exposed to BAC at 160 mg/L (concentration above the MBC) showed significant reductions on all the evaluated indicators. However, the obtained values were much higher than the 'death' thresholds found for the autoclaved cells. This suggests that cells exposed to this concentration take more time to rebuild their functional processes. The recovery of DBNPA-treated cells did not seem to be related to the biocide concentration. Finally, a reflection on what kind of cells were able to recover (remaining cells below the detection limit and/or dormant cells) is also presented.

Transcriptome Analysis of Viable but Non-Culturable Brettanomyces bruxellensis Induced by Hop Bitter Acids

The viable but non-culturable (VBNC) state has been studied in detail in bacteria. However, it has received much less attention in eukaryotic cells. The induction of a VBNC beer-spoilage yeast (Brettanomyces bruxellensis) by hop bitter acids with different concentrations and its recovery were studied in this work. B. bruxellensis cells were completely induced into the VBNC state by treatment of 250 mg/L hop bitter acids for 2 h. The addition of catalase at a concentration of 2,000 U/plate on YPD agars enabled these VBNC cells to recover their culturability within 2 days. Moreover, the transcriptome profiling revealed that 267 and 197 genes were significantly changed upon VBNC state entry and resuscitation, respectively. The differentially expressed genes involved in the peroxisome activities, ABC transporter, organic acid metabolism, and TCA cycle were mainly downregulated in the VBNC cells. In contrast, the amino acid and carbohydrate metabolism, cell division, and DNA replication were promoted. This study supplies a theoretical basis for microbial risk assessment in the brewing industry.

Oxidative dehalogenation and mineralization of polychlorinated biphenyls by a resuscitated strain Streptococcus sp. SPC0

Most functional microorganisms cannot be cultivated due to entering a viable but non-culturable (VBNC) state, which limits the characterization and application of polychlorinated biphenyl (PCB)-degrading strains. Resuscitating VBNC bacteria could provide huge candidates for obtaining high-efficient PCB degraders. However, limited studies have focused on the ability of resuscitated strains for PCBs degradation. In the present study, whole-genome analysis of a resuscitated strain SPC0, and its performances in degradation of three prevalent PCB congeners (PCBs 18, 52 and 77) were investigated. The results indicate that the strain SPC0 belonged to the genus Streptococcus, possessed the degradation potential for aromatic xenobiotics. The SPC0 could effectively degrade PCBs 18 and 52, but exhibited lower degradation efficiency of PCB 77. Degradation of PCBs 18 and 52 could be fitted well by zero-order model, whereas the fittest model for PCB 77 degradation was pseudo second-order kinetics. The bph genes expression, chloride ions release and degradation metabolites identification, suggest that SPC0 possessed the capability of oxidative dehalogenation and mineralization of PCBs. Interestingly, SPC0 can degrade PCBs via the bph-encoded biphenyl pathway, and further mineralize metabolite dichlorobenzoate via protocatechuate pathway. This study is the first to show that a strain belonging to genus Streptococcus possessed PCB-degrading capability, which uncovered the powerful potential of resuscitated strains for bioremediation of PCB-contaminated sites.

Pangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9

Environmental bacteria contain a wealth of untapped potential in the form of biodegradative genes. Leveraging this potential can often be confounded by a lack of understanding of fundamental survival strategies, like dormancy, for environmental stress. Investigating bacterial dormancy-to-degradation relationships enables improvement of bioremediation. Here, we couple genomic and functional assessment to provide context for key attributes of the organic pollutant-degrading strain Rhodococcus biphenylivorans TG9. Whole genome sequencing, pangenome analysis and functional characterization were performed to elucidate important genes and gene products, including antimicrobial resistance, dormancy, and degradation. Rhodococcus as a genus has strong potential for degradation and dormancy, which we demonstrate using R. biphenylivorans TG9 as a model. We identified four Resuscitation-promoting factor (Rpf) encoding genes in TG9 involved in dormancy and resuscitation. We demonstrate that R. biphenylivorans TG9 grows on fourteen typical organic pollutants, and exhibits a robust ability to degrade biphenyl and several congeners of polychlorinated biphenyls. We further induced TG9 into a dormant state and demonstrated pronounced differences in morphology and activity. Together, these results expand our understanding of the genus Rhodococcus and the relationship between dormancy and biodegradation in the presence of environmental stressors.

Success of microbial genes based transgenic crops: Bt and beyond Bt

Transgenic technology could hold the key to help farmers to fulfill the ever increasing fast-paced global demand for food. Microbes have always wondered us by their potentials and thriving abilities in the extreme conditions. The use of microorganisms as a gene source in transgenic development is a promising option for crop improvement. The aforesaid approach has already for improving the characteristics of food, industrial, horticulture, and floriculture crops. Many transgenic crops containing microbial genes have been accepted by the farmers and consumers worldwide over the last few decades. The acceptance has brought remarkable changes in the status of society by providing food safety, economic, and health benefits. Among transgenic plants harboring microbial genes, Bacillus thuringiensis (Bt) based transgenic were more focused and documented owing to its significant performance in controlling insects. However, other microbial gene-based transgenic plants have also reserved their places in the farmer's field globally. Therefore, in this review, we have thrown some light on successful transgenic plants harboring microbial genes other than Bt, having application in agriculture. Also, we presented the role of microbial genetic element and product thereof in the inception of biotechnology and discussed the potential of microbial genes in crop improvement.

The conversion of the nutrient condition alter the phenol degradation pathway by Rhodococcus biphenylivorans B403: A comparative transcriptomic and proteomic approach

Highly toxic phenol causes a threat to the ecosystem and human body. The development of bioremediation is a crucial issue in environmental protection. Herein, Rhodococcus biphenylivorans B403, which was isolated from the activated sludge of the sewage treatment plant, exhibited a good tolerance and removal efficiency to phenol. The degradation efficiency of phenol increased up to 62.27% in the oligotrophic inorganic medium (MM) containing 500-mg/L phenol at 18 h. R. biphenylivorans B403 cultured in the MM medium showed a higher phenol degradation efficiency than that in the eutrophic LB medium. On the basis of the transcriptomic and proteomic analysis, a total of 799 genes and 123 proteins showed significantly differential expression between two different culture conditions, especially involved in phenol degradation, carbon metabolism, and nitrogen metabolism. R. biphenylivorans B403 could alter the phenol degradation pathway by facing different culture conditions. During the phenol removal in the oligotrophic inorganic medium, muconate cycloisomerase, acetyl-CoA acyltransferase, and catechol 1,2-dioxygenase in the ortho-pathway for phenol degradation showed upregulation compared with those in the eutrophic organic medium. Our study provides novel insights into the possible pathway underlying the response of bacterium to environmental stress for phenol degradation.

Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants

Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg^-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.

Viable but Nonculturable State of Yeast Candida sp. Strain LN1 Induced by High Phenol Concentrations

Microbial degradation plays an important role in environmental remediation. However, most microorganisms' pollutant-degrading capabilities are weakened due to their entry into a viable but nonculturable (VBNC) state. Although there is some evidence for the VBNC state of pollutant-degrading bacteria, limited studies have been conducted to investigate the VBNC state of pollutant degraders among fungi. In this work, the morphological, physiological, and molecular changes of phenol-degrading yeast strain LN1 exposed to high phenol concentrations were investigated. The results confirmed that Candida sp. strain LN1, which possessed a highly efficient capability of degrading 1,000 mg/liter of phenol as well as a high potential for aromatic compound degradation, entered into the VBNC state after 14 h of incubation with 6,000 mg/liter phenol. Resuscitation of VBNC cells can restore their phenol degradation performance. Compared to normal cells, significant dwarfing, surface damage, and physiological changes of VBNC cells were observed. Molecular analysis indicated that downregulated genes were related to the oxidative stress response, xenobiotic degradation, and carbohydrate and energy metabolism, whereas upregulated genes were related to RNA polymerase, amino acid metabolism, and DNA replication and repair. This report revealed that a pollutant-degrading yeast strain entered into the VBNC state under high concentrations of contaminants, providing new insights into its survival status and bioremediation potential under stress. IMPORTANCE The viable but nonculturable (VBNC) state is known to affect the culturability and activity of microorganisms. However, limited studies have been conducted to investigate the VBNC state of other pollutant degraders, such as fungi. In this study, the VBNC state of a phenol-degrading yeast strain was discovered. In addition, comprehensive analyses of the morphological, physiological, and molecular changes of VBNC cells were performed. This study provides new insight into the VBNC state of pollutant degraders and how they restored the activities that were inhibited under stressful conditions. Enhanced bioremediation performance of indigenous microorganisms could be expected by preventing and controlling the formation of the VBNC state.

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.

The classification of bacterial survival strategies in the presence of antimicrobials

The survival of bacteria under antibiotic therapy varies in nature and is based on the bacterial ability to employ a wide range of fundamentally different resistance mechanisms. This great diversity requires a disambiguation of the term 'resistance' and the development of a more precise classification of bacterial survival strategies during contact with antibiotics. The absence of a unified definition for the terms 'resistance', 'tolerance' and 'persistence' further aggravates the imperfections of the current classification system. This review suggests a number of original classification criteria that will take into account (1) the bacterial ability to replicate in the presence of antimicrobial agents, (2) existing evolutionary stability of a trait within a species, and (3) the presence or absence of specialized genes that determine the ability of a microorganism to decrease its own metabolism or switch it completely off. This review describes potential advantages of the suggested classification system, which include a better understanding of the relationship between bacterial survival in the presence of antibiotics and molecular mechanisms of cellular metabolism suppression, the opportunity to pinpoint targets to identify a true bacterial resistance profile. The true resistance profile in turn, could be used to develop effective diagnostic and antimicrobial therapy methods, while taking into consideration specific bacterial survival mechanisms.

Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms

Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation.

Anaerobic condition induces a viable but nonculturable state of the PCB-degrading Bacteria Rhodococcus biphenylivorans TG9

Significant microbial removal of highly chlorinated polychlorinated biphenyls (PCBs) requires the cooperation of anaerobic and aerobic bacteria. During the sequencing process of anaerobic dechlorination and aerobic degradation of PCBs, aerobic degrading bacteria have to undergo anaerobic stress. However, the survival strategy of aerobic degrading bacteria under anaerobic condition is not well-understood. In this study, the culturable cells of Rhodococcus biphenylivorans TG9 decreased from 10⁸ CFU/mL to values below the detection limit after 60 days of anaerobic stress while the viable cells remained 10⁵-10⁶ cells/mL, indicating that anaerobic condition induced TG9 entering into the viable but nonculturable (VBNC) state. Cell resuscitation was observed when oxygen was supplied further confirming the VBNC state of TG9. The results of single-cell Raman spectroscopy combined with heavy water indicated the significant decrease of metabolic activity after TG9 entering into the VBNC state. Additionally, the degradation ability of TG9 in the VBNC state was also significantly reduced, while it recovered after resuscitation. Our research proved that entering into the VBNC state is a survival strategy of TG9 under anaerobic conditions, and the limited culturability and degrading capacity could be overcome by resuscitation. The present study provides new insights for improving the remediation efficiency of PCBs contamination.

Environmental Management of Legionella in Domestic Water Systems: Consolidated and Innovative Approaches for Disinfection Methods and Risk Assessment

Legionella is able to remain in water as free-living planktonic bacteria or to grow within biofilms that adhere to the pipes. It is also able to enter amoebas or to switch into a viable but not culturable (VBNC) state, which contributes to its resistance to harsh conditions and hinders its detection in water. Factors regulating Legionella growth, such as environmental conditions, type and concentration of available organic and inorganic nutrients, presence of protozoa, spatial location of microorganisms, metal plumbing components, and associated corrosion products are important for Legionella survival and growth. Finally, water treatment and distribution conditions may affect each of these factors. A deeper comprehension of Legionella interactions in water distribution systems with the environmental conditions is needed for better control of the colonization. To this purpose, the implementation of water management plans is the main prevention measure against Legionella. A water management program requires coordination among building managers, health care providers, and Public Health professionals. The review reports a comprehensive view of the state of the art and the promising perspectives of both monitoring and disinfection methods against Legionella in water, focusing on the main current challenges concerning the Public Health sector.

Role of amoebae for survival and recovery of 'non-culturable' Helicobacter pylori cells in aquatic environments

Helicobacter pylori is a fastidious Gram-negative bacterium that infects over half of the world's population, causing chronic gastritis and is a risk factor for stomach cancer. In developing and rural regions where prevalence rate exceeds 60%, persistence and waterborne transmission are often linked to poor sanitation conditions. Here we demonstrate that H. pylori not only survives but also replicates within acidified free-living amoebal phagosomes. Bacterial counts of the clinical isolate H. pylori G27 increased over 50-fold after three days in co-culture with amoebae. In contrast, a H. pylori mutant deficient in a cagPAI gene (cagE) showed little growth within amoebae, demonstrating the likely importance of a type IV secretion system in H. pylori for amoebal infection. We also demonstrate that H. pylori can be packaged by amoebae and released in extracellular vesicles. Furthermore, and for the first time, we successfully demonstrate the ability of two free-living amoebae to revert and recover viable but non-cultivable coccoid (VBNC)-H. pylori to a culturable state. Our studies provide evidence to support the hypothesis that amoebae and perhaps other free-living protozoa contribute to the replication and persistence of human-pathogenic H. pylori by providing a protected intracellular microenvironment for this pathogen to persist in natural aquatic environments and engineered water systems, thereby H. pylori potentially uses amoeba as a carrier and a vector of transmission.

Stress response in Rhodococcus strains

Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.

The diagnostic tools for viable but nonculturable pathogens in the food industry: Current status and future prospects

Viable but nonculturable (VBNC) microorganisms have been recognized as pathogenic contaminants in foods and environments. The failure of VBNC cells to form the visible colonies hinders the ability to use conventional media for their detection. Efficient and rapid detection of pathogens in the VBNC state is a prerequisite to ensure the food safety and public health. Despite their nonculturability, VBNC cells have distinct characteristics, such as morphology, metabolism, chemical composition, and gene and protein expression, that have been used as the basis for the development of abundant diagnostic tools. This review covers the current status and advances in various approaches for examining microorganisms in the VBNC state, including but not limited to the methodological aspects, advantages, and drawbacks of each technique. Existing methods, such as direct viable count, SYTO/PI dual staining, and propidium monoazide quantitative polymerase chain reaction (PCR), as well as some techniques with potential to be applied in the future, such as digital PCR, enhanced-surface Raman spectroscopy, and impedance-based techniques, are summarized in depth. Finally, future prospects for the one-step detection of VBNC bacteria are proposed and discussed. We believe that this review can provide more optional methods for researchers and promote the development of rapid, accurate detecting methods, and for inspectors, the diagnostic tools can provide data to undertake risk analysis of VBNC cells.

Enhancement of polychlorinated biphenyl biodegradation by resuscitation promoting factor (Rpf) and Rpf-responsive bacterial community

The activities of indigenous bacterial communities in polychlorinated biphenyls (PCBs) contaminated environments is closely related to the efficiency of bioremediation processes. Using resuscitation promoting factor (Rpf) from Micrococcus luteus is a promising method for resuscitation and stimulation of functional bacterial populations under stressful conditions. This study aims to use the Rpf to accelerate the biodegradation of Aroclor 1242, and explore putative PCB degraders which were resuscitated by Rpf addition. The Rpf-responsive bacterial populations were investigated using culture-dependent and culture-independent approaches, respectively. The results confirm that Rpf was capable of enhancing PCB degradation of enriched cultures from PCB-contaminated soils, and improving the activities of cultures with low tolerance to PCBs. High-throughput 16S rRNA analysis displays that the Rpf greatly altered the composition and abundance of bacterial populations in the phylum Proteobacteria. Identification of the resuscitated strains further suggests that the Rpf-responsive population was mostly represented by Sphingomonas and Pseudomonas, which are most likely the key PCB-degraders for enhanced biodegradation of PCBs.

Alterations in the Cell Wall of Rhodococcus biphenylivorans Under Norfloxacin Stress

Many microorganisms can enter a viable but non-culturable (VBNC) state under various environmental stresses, while they can also resuscitate when the surroundings turn to suitable conditions. Cell walls play a vital role in maintaining cellular integrity and protecting cells from ambient threats. Here, we investigated the alterations in the cell wall of Rhodococcus biphenylivorans TG9 at VBNC state under norfloxacin stress and then at resuscitated state in fresh lysogeny broth medium. Electron microscopy analyses presented that TG9 in the VBNC state had a thicker and rougher cell wall than that in exponential phase or resuscitated state. Meanwhile, the results from infrared spectroscopy also showed that its VBNC state has different peptidoglycan structures in the cell wall. Moreover, in the VBNC cells the gene expressions related to cell wall synthesis and remodeling maintain a relatively high level. It indicates that the morphological variations of TG9 at the VBNC state might result from kinetic changes in the cell wall synthesis and remodeling. As a consequence, the alterations in the cell wall of VBNC TG9 may somewhat account for its tolerance mechanisms to antibiotic treatment.

Resuscitation, isolation and immobilization of bacterial species for efficient textile wastewater treatment: A critical review and update

Given highly complex and recalcitrant nature of synthetic dyes, textile wastewater poses a serious challenge on surrounding environments. Until now, biological treatment of textile wastewater using efficient bacterial species is still considered as an environmentally friendly and cost-effective approach. The advances in resuscitating viable but non-culturable (VBNC) bacteria via signaling compounds such as resuscitation-promoting factors (Rpfs) and quorum sensing (QS) autoinducers, provide a vast majority of potent microbial resources for biological wastewater treatment. So far, textile wastewater treatment from resuscitating and isolating VBNC state bacteria has not been critically reviewed. Thus, this review aims to provide a comprehensive picture of resuscitation, isolation and application of bacterial species with this new strategy, while the recent advances in synthetic dye decolorization were also elaborated together with the mechanisms involved. Discussion was further extended to immobilization methods to tackle its application. We concluded that the resuscitation of VBNC bacteria via signaling compounds, together with biochar-based immobilization technologies, may lead to an appealing biological treatment of textile wastewater. However, further development and optimization of the integrated process are still required for their wide applications.

Comparison of Two Inoculation Methods of Endophytic Bacteria to Enhance Phytodegradation Efficacy of an Aged Petroleum Hydrocarbons Polluted Soil

Endophyte-enhanced phytodegradation is a promising technology to clean up polluted soils. To improve the success rate of this nature-based remediation approach, it is important to advance the inoculation method as this has been shown to strongly affect the final outcome. However, studies evaluating inoculation strategies and their effect on hydrocarbon degradation are limited. This study aims to investigate two different manners of endophyte inoculation in Lolium perenne growing in an aged petroleum hydrocarbon polluted soil: (1) direct soil inoculation (SI), and (2) pre-inoculation of the caryopses followed by soil inoculation (PI). Different endophytic bacterial strains, Rhodococcus erythropolis 5WK and Rhizobium sp. 10WK, were applied individually as well as in combination. Depending on the method of inoculation, the petroleum hydrocarbon (PHC) degradation potential was significantly different. The highest PHC removal was achieved after pre-inoculation of ryegrass caryopses with a consortium of both bacterial strains. Moreover, both strains established in the aged-polluted soil and could also colonize the roots and shoots of L. perenne. Importantly, used endophytes showed the selective colonization of the environment compartments. Our findings show that the method of inoculation determines the efficiency of the phytodegradation process, especially the rate of PHC degradation. This study provides valuable information for choosing the most cost-effective and beneficial means to optimize phytodegradation.

Supplementing resuscitation-promoting factor (Rpf) enhanced biodegradation of polychlorinated biphenyls (PCBs) by Rhodococcus biphenylivorans strain TG9T

The biodegradation of polychlorinated biphenyls (PCBs) occurs slowly when the degrading bacteria enter a low activity state, such as a viable but nonculturable (VBNC) state, under unfavorable environmental conditions. The introduction of resuscitation-promoting factor (Rpf) can re-activate VBNC bacteria. This study tested the feasibility of enhancing PCB biodegradation via supplementing Rpf in liquid culture and soil microcosms inoculated with Rhodococcus biphenylivorans strain TG9^T. Exogenous Rpf resuscitated TG9^T cells that had previously entered the VBNC state after 90 d of nutrient starvation, resulting in the significantly enhanced degradation of PCB by 24.3% over 60 h in liquid medium that originally contained 50 mg L^-1 Aroclor 1242. In soil microcosms containing 50 mg kg^-1 Aroclor 1242 and inoculated with VBNC TG9^T cells, after 49 d of supplementation with Rpf, degradation efficiency of PCB reached 34.2%, which was significantly higher than the control. Our results confirmed that exogenous Rpf resuscitated VBNC TG9^T cells by stimulating endogenous expression of rpf gene orthologs. The enhanced PCB-degrading capability was likely due to the increased cell numbers and the strong expression of PCB catabolic genes. This study demonstrated the role of Rpf in enhancing PCB degradation via resuscitating PCB-degrading bacteria, indicating a promising approach for the remediation of PCB contamination.

Intensification of Ex Situ Bioremediation of Soils Polluted with Used Lubricant Oils: A Comparison of Biostimulation and Bioaugmentation with a Special Focus on the Type and Size of the Inoculum

Used lubricant oils (ULOs) strongly bind to soil particles and cause persistent pollution. In this study, soil microcosm experiments were conducted to model the ex situ bioremediation of a long term ULO-polluted area. Biostimulation and various inoculation levels of bioaugmentation were applied to determine the efficacy of total petrol hydrocarbon (TPH) removal. ULO-contaminated soil microcosms were monitored for microbial respiration, colony-forming units (CFUs) and TPH bioconversion. Biostimulation with inorganic nutrients was responsible for 22% of ULO removal after 40 days. Bioaugmentation using two hydrocarbon-degrader strains: Rhodococcus quingshengii KAG C and Rhodococcus erythropolis PR4 at a small inoculum size (107 CFUs g-1 soil), reduced initial TPH concentration by 24% and 29%, respectively; the application of a higher inoculum size (109 CFUs g-1 soil) led to 41% and 32% bioconversion, respectively. After 20 days, all augmented CFUs decreased to the same level as measured in the biostimulated cases, substantiating the challenge for the newly introduced hydrocarbon-degrading strains to cope with environmental stressors. Our results not only highlight that an increased number of degrader cells does not always correlate with enhanced TPH bioconversion, but they also indicate that biostimulation might be an economical solution to promote ULO biodegradation in long term contaminated soils.

Characterization and potential mechanisms of highly antibiotic tolerant VBNC Escherichia coli induced by low level chlorination

Escherichia coli is an important pathogenic indicator in drinking water. Viable but non-culturable (VBNC) E. coli induced by low level chlorination was found to have higher antibiotic tolerance. The emerging of VBNC bacteria in drinking water systems is posing challenges to the control of bio-safety. It is necessary to study the underlying mechanisms of VBNC state E. coli under actual residual chlorine condition of drinking water pipe network. In this study, we investigated the changes of morphology and gene expressions that might present such state. The results indicated that the size of VBNC E. coli was not remarkably changed or recovered culturability under favorable environmental conditions. Results from transcriptomic analysis revealed that the regulated genes related to fimbrial-like adhesin protein, putative periplasmic pilin chaperone, regulators of the transcriptional regulation, antibiotic resistance genes and stress-induced genes, rendering VBNC cells more tolerant to adverse environmental conditions. In total of 16 genes were significantly up-regulated under the VBNC state, including three genes encoding toxic protein (ygeG, ibsD, shoB), indicating that VBNC E. coil was still a threat to human. The work is of great relevance in the context of better understanding this poorly understood physiological state.

Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices

The persistence of bacterial pathogens within environmental matrices plays an important role in the epidemiology of diseases, as well as impacts biosurveillance strategies. However, the adaptation potentials, mechanisms for survival, and ecological interactions of pathogenic bacteria such as Yersinia pestis are largely uncharacterized owing to the difficulty of profiling their phenotypic signatures. In this report, we describe studies on Y. pestis organisms cultured within soil matrices, which are among the most important reservoirs for their propagation. Morphological (nanoscale) and phenotypic analysis are presented at the single cell level conducted using Atomic Force Microscopy (AFM), coupled with biochemical profiles of bulk populations using Fatty Acid Methyl Ester Profiling (FAME). These studies are facilitated by a novel, customizable, 3D printed diffusion chamber that allows for control of the external environment and easy harvesting of cells. The results show that incubation within soil matrices lead to reduction of cell size and an increase in surface hydrophobicity. FAME profiles indicate shifts in unsaturated fatty acid compositions, while other fatty acid components of the phospholipid membrane or surface lipids remained consistent across culturing conditions, suggesting that phenotypic shifts may be driven by non-lipid components of Y. pestis.