A novel strategy for enhancing bioremediation of polychlorinated biphenyl-contaminated soil with resuscitation promoting factor and resuscitated strain

Resuscitation of viable but nonculturable bacteria promoted by ATP-mediated NAD+ synthesis

INTRODUCTION

Entry into the viable but nonculturable (VBNC) state is a survival strategy adopted by bacteria to survive harsh environment. Although VBNC cells still have metabolic activity, they lose the ability to form colonies on nonselective culture media. Thus, conventional bacterial detection methods, such as plate counting, are unable to detect the presence of VBNC cells. When the environmental conditions are appropriate, VBNC cells can initiate resuscitation, posing a great risk to the safety of public health. The study of the VBNC resuscitation mechanism could provide new insights into the prevention and control of VBNC resuscitation.

OBJECTIVES

Uncovering the molecular mechanism of VBNC cell resuscitation by investigating the role of O-antigen ligase (RfaL) in inhibiting the resuscitation of Escherichia coli O157:H7 in the VBNC state.

METHODS

RfaL was screened and verified as a resuscitation inhibitor of VBNC Escherichia coli O157:H7 by detecting resuscitation curve and time-lapse microscopy. The mechanism of RfaL impacts VBNC E. coli resuscitation was investigated by detecting the single cell ATP content, metabolomic changes, NAD(H) content and new protein biosynthesis of WT and ΔrfaL at different stage of resuscitation.

RESULTS

Mutation of rfaL, which encoded an O-antigen ligase, markedly shortened the resuscitating lag phase. Further studies indicated that ΔrfaL VBNC cells contained higher ATP levels, and ATP consumption during the resuscitating lag phase was highly correlated with resuscitation efficiency. Metabolomic analysis revealed that ATP was utilized to activate the Handler and salvage pathways to synthesize NAD+, balancing redox reactions to recover cell activity and promote cell resuscitation.

CONCLUSION

Our findings revealed a strategy employed by VBNC cells for revival, that is, using residual ATP to primarily recover metabolic activity, driving cells to exit dormancy. The synthesis pathway of lipopolysaccharide (LPS) in rfaL null mutant was inhibited and could supply more ATP to synthesis NAD+ and promote resuscitation.

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.

Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.

An alkali-enhanced subcritical water treatment strategy of short-chain chlorinated paraffins: Dechlorination and hydrocarbons recovery

As persistent organic pollutants, short-chain chlorinated paraffins (SCCPs) have attracted wide attention in the field of environmental health risk and hazardous waste management. Efficient dechlorination of high content of SCCPs in plastic waste is the committed step for its detoxification and safety treatment. In this study, a high-efficiency and low-temperature process for dechlorination and hydrocarbons recovery from typical SCCPs (52#SCCPs) by subcritical water (SubCW) with alkali enhancer was developed. The introduction of alkali enhancer in the SubCW process had significantly enhanced effect on the dechlorination of 52#SCCPs, and the order of the enhanced effect of alkali enhancer for the dechlorination was NaOH > Na2CO3 > NaHCO3 > NH3·H2O > KOH. The dechlorination behaviors of 52#SCCPs in the NaOH-enhanced SubCW process were studied systematically under different conditions including temperature, residence time, alkali concentration, and volume ratio. The results showed that high-efficiency dechlorination (100 %) of 52#SCCPs could be achieved by the NaOH-enhanced SubCW process at low temperature for a short time (250 °C, 5 min). All of the chlorine released from the molecular chain of 52#SCCPs was transferred to the aqueous phase in the form of inorganic chlorine. The continuous HCl elimination reaction was the primary dechlorination mechanism for 52#SCCPs in the NaOH-enhanced SubCW process. After the dechlorination of 52#SCCPs, high value-added hydrocarbons such as 2,4-hexadiyne (31.74 %) could be obtained. The alkali-enhanced SubCW process proposed in this study is believed to be an environmentally friendly and high-efficiency method for dechlorination/detoxification and resource recovery of SCCPs.

Anaerobic biodegradation of azo dye reactive black 5 by a novel strain Shewanella sp. SR1: Pathway and mechanisms

The efficiency of microbial populations in degrading refractory pollutants and the impact of adverse environmental factors often presents challenges for the biological treatment of azo dyes. In this study, the genome analysis and azo dye Reactive Black 5 (RB5) degrading capability of a newly isolated strain, Shewanella sp. SR1, were investigated. By analyzing the genome, functional genes involved in dye degradation and mechanisms for adaptation to low-temperature and high-salinity conditions were identified in SR1. The addition of co-substrates, such as glucose and yeast extract, significantly enhanced RB5 decolorization efficiency, reaching up to 87.6%. Notably, SR1 demonstrated remarkable robustness towards a wide range of NaCl concentrations (1-30 g/L) and temperatures (10-30 °C), maintaining efficient decolorization and high biomass concentration. The metabolic pathways of RB5 degradation were deduced based on the metabolites and genes detected in the genome, in which the azo bond was first cleaved by FMN-dependent NADH-azoreductase and NAD(P)H-flavin reductase, followed by deamination, desulfonation, and hydroxylation mediated by various oxidoreductases. Importantly, the degradation metabolites exhibited reduced toxicity, as revealed by toxicity analysis. These findings highlighted the great potential of Shewanella sp. SR1 for bioremediation of wastewaters contaminated with azo dyes.

Mechanistic insight into lead immobilization on bone-derived carbon/hydroxyapatite composite at low and high initial lead concentration

The contamination of heavy metal lead has a serious impact on the natural environment and organisms. Among various materials for lead removal, animal bone derived hydroxyapatite has received extensive attention. However, there are different opinions among researchers regarding the mechanism of lead removal by hydroxyapatite, possibly due to varying initial lead concentrations used in different studies and lack of accuracy in the study of lead removal mechanisms. In present work, we synthesized a carbon-containing hydroxyapatite (CHAP) through pyrolysis of bovine bone with excellent lead removal efficiency, and further investigated the lead removal mechanism of CHAP under high and low initial lead concentrations by combining XRD Rietveld refinement, FTIR, XPS, HRTEM etc. methods. The results showed that under low initial Pb2+ concentration condition, the main mechanism of lead removal by CHAP was chemical precipitation (94.1 %), with small contributions of lead complexation with carbon functional groups and cation-π interactions on the amorphous carbon in CHAP, and surface adsorption on the precipitates. Under high initial Pb2+ concentration condition, chemical precipitation remained the main mechanism (74.68 %), but the contributions of the other three mechanisms increased, and ion exchange appeared in the later stage of the removal process. This study provides new insights on the lead immobilization mechanism by CHAP at different initial Pb2+ concentrations in water.

Unlocking the potential of resuscitation-promoting factor for enhancing anaerobic microbial dechlorination of polychlorinated biphenyls

Microbial dechlorination of polychlorinated biphenyls (PCBs) is limited by the slow growth rate and low activity of dechlorinators. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been demonstrated to accelerate the enrichment of highly active PCB-dechlorinating cultures. However, it remains unclear whether the addition of Rpf can further improve the dechlorination performance of anaerobic dechlorination cultures. In this study, the effect of Rpf on the performance of TG4, an enriched PCB-dechlorinating culture obtained by Rpf amendment, for reductive dechlorination of four typical PCB congeners (PCBs 101, 118, 138, 180) was evaluated. The results indicated that Rpf significantly enhanced the dechlorination of the four PCB congeners, with residual mole percentages of PCBs 101, 118, 138 and 180 in Rpf-amended cultures being 16.2-29.31 %, 13.3-20.1 %, 11.9-14.4 % and 9.4-17.3 % lower than those in the corresponding cultures without Rpf amendment after 18 days of incubation. Different models were identified as appropriate for elucidating the dechlorination kinetics of distinct PCB congeners, and it was observed that the dechlorination rate constant is significantly influenced by the PCB concentration. The supplementing Rpf did not obviously change dechlorination metabolites, and the removal of chlorines occurred mainly at para- and meta- positions. Analysis of microbial community and functional gene abundance suggested that Rpf-amended cultures exhibited a significant enrichment of Dehalococcoides, Dehalogenimonas and Desulfitobacterium, as well as non-dechlorinators belonging to Desulfobacterota and Bacteroidetes. These findings highlight the potential of Rpf as an effective additive for enhancing PCB dechlorination, providing new insights into the survival of functional microorganisms involved in anaerobic reductive dechlorination.

Efficient pyridine biodegradation by Stenotrophomonas maltophilia J2: Degradation performance, mechanism, and immobilized application for wastewater

Stenotrophomonas maltophilia J2, a highly efficient pyridine-degrading bacterium, was isolated from the aerobic tank of a pesticide-contaminated wastewater treatment plant. The strain J2 demonstrated an impressive pyridine degradation rate of 98.34% ± 0.49% within 72 h, at a pyridine concentration of 1100 mg·L-1, a temperature of 30 °C, a pH of 8.0, and a NaCl concentration of 0.5%. Notably, two new pyridine metabolic intermediates, 1,3-dihydroxyacetone and butyric acid, were discovered, indicating that J2 may degrade pyridine through two distinct metabolic pathways. Furthermore, the immobilized strain J2 was obtained by immobilizing J2 with biochar derived from the stem of Solidago canadensis L. In the pyridine-contaminated wastewater bioremediation experiment, the immobilized strain J2 was able to remove 2000 mg·L-1 pyridine with a 98.66% ± 0.47% degradation rate in 24 h, which was significantly higher than that of the control group (3.17% ± 1.24%), and remained above 90% in subsequent cycles until the 27th cycle. High-throughput sequencing analysis indicated that the J2 +B group had an elevated relative abundance of bacteria and functional genes that could be associated with the degradation of pyridine. The results offer a foundation for the effective use of immobilized strain in the treatment of recalcitrant pyridine-contaminated wastewater.

Effect of quorum quenching on biofouling control and microbial community in membrane bioreactors by Brucella sp. ZJ1

Quorum quenching (QQ) has been demonstrated to be a novel technique for controlling biofouling in membrane bioreactors (MBRs), as it can significantly inhibit biofilm formation by disrupting quorum sensing (QS). The exploration of new QQ bacterial strains and the evaluation of their performance in mitigating membrane fouling in MBR systems is significant. In this study, an efficient QQ strain, Brucella sp. ZJ1 was encapsulated in alginate beads and evaluated for its ability to mitigate biofouling. The findings revealed that MBR with QQ beads extended the operation time by 2-3 times without affecting pollutant degradation. QQ beads maintained approximately 50% QQ activity after more than 50 days operation, indicating a long-lasting and endurable QQ effect. The QQ effect reduced extracellular polymeric substance (EPS) production especially in terms of polysaccharide and protein by more than 40%. QQ beads in the MBR also reduced the cake resistance and the irreversible resistance of membrane biofouling. Metagenomic sequencing suggests that QQ beads suppressed the QS effect and increased the abundance of QQ enzyme genes, ultimately inducing efficient membrane biofouling control.

Nitenpyram biodegradation by a novel nitenpyram-degrading bacterium, Ochrobactrum sp. strain DF-1, and its novel degradation pathway

Nitenpyram is a neonicotinoid insecticide that is commonly found in the environment. However, its biodegradation by pure cultures of bacteria has not been widely investigated and the catabolic pathway (s) for nitenpyram metabolism remain elusive. In this study, the aerobic strain DF-1, isolated from a wastewater-treatment pool contaminated with nitenpyram. The strain was designated an Ochrobactrum sp. utilizing a combination of traditional methods and molecular ones. Strain DF-1 can use nitenpyram as a sole carbon or nitrogen source for growth. In liquid medium, 100 mg·L^-1 nitenpyram was metabolized to undetectable levels within 10 days. Four metabolites were found by gas chromatography-mass spectrometry (GC-MS) analyses during nitenpyram degradation. According to the aforementioned data, a partial metabolic pathway of nitenpyram was proposed of strain DF-1. Inoculation of strain DF-1 promoted nitenpyram (10 mg·kg^-1) degradation in either sterile or non-sterile soil. To our knowledge, this is the first characterization of nitenpyram degradation by a specific bacterium and likely to be exploited for the remediation of nitenpyram-contaminated sites.

Triclocarban-contaminated wastewater treatment by innovative hybrid moving entrapped bead activated sludge reactor (HyMER): Continuous performance and computational dynamic simulation analysis

Triclocarban (TCC) has been used in consumer products and is a widespread contaminant in municipal wastewater treatment systems that ultimately accumulates in natural receiving water and soil. This work aims to apply an innovative hybrid moving entrapped bead activated sludge reactor (named "HyMER") that integrates entrapped TCC-degrading microbes and freely suspended activated sludge to treat TCC-contaminated wastewater. A previously isolated TCC-degrading bacterium (Pseudomonas fluorescens strain MC46, called MC46) and barium alginate entrapment were applied. The synthetic TCC-contaminated wastewater treatment (with TCC concentration of 10 mg/L) was performed using 20-cycle fed-batch reactor operation with feeding times of 12 and 24 h and cycle times of 13 and 25 h. The results indicated that the HyMER effectively reduced chemical oxygen demand by up to 80 and 95 % and TCC by up to 53 and 83 %, respectively, with feeding times of 12 and 24 h. Three TCC degradation intermediate products were found-3,4-dichloroaniline, 4-chloroaniline, and aniline. Scanning electron microscopic analysis revealed shorter cells and bacterial appendage development as cell adaptations against TCC and its intermediates. The live/dead assay indicated high survival of entrapped MC46 in toxic conditions, with up to 84 % viable cells. Based on computational fluid dynamic analysis, no entrapped cell agglomeration showed in the reactor, indicating the potential application of HyMER for real wastewater treatment. These results exhibit the feasibility of HyMER and its applicability for future toxic wastewater treatment.

Photo-aging promotes the inhibitory effect of polystyrene microplastics on microbial reductive dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Polychlorinated biphenyls (PCBs) and microplastics (MPs) commonly co-exist in various environments. MPs inevitably start aging once they enter environment. In this study, the effect of photo-aged polystyrene MPs on microbial PCB dechlorination was investigated. After a UV aging treatment, the proportion of oxygen-containing groups in MPs increased. Photo-aging promoted the inhibitory effect of MPs on microbial reductive dechlorination of PCBs, mainly attributed to the inhibition of meta-chlorine removal. The inhibitory effects on hydrogenase and adenosine triphosphatase activity by MPs increased with increasing aging degree, which may be attributed to electron transfer chain inhibition. PERMANOVA showed significant differences in microbial community structure between culturing systems with and without MPs (p < 0.05). Co-occurrence network showed a simpler structure and higher proportion of negative correlation in the presence of MPs, especially for biofilms, resulting in increased potential for competition among bacteria. MP addition altered microbial community diversity, structure, interactions, and assembly processes, which was more deterministic in biofilms than in suspension cultures, especially regarding the bins of Dehalococcoides. This study sheds light on the microbial reductive dechlorination metabolisms and mechanisms where PCBs and MPs co-exist and provides theoretical guidance for in situ application of PCB bioremediation technology.