Stress responses of Acinetobacter strain Y during phenol degradation

Virus-bacterium interaction involved in element cycles in biological treatment of coking wastewater

Although prokaryotic microbes in coking wastewater (CWW) treatment have been comprehensively studied, the ecological functions of viruses remain unclear. A full-scale CWW biological treatment AOHO combination was studied for the virus-bacterium interactions involved in element cycles by metaviromics, metagenomics and physicochemical characteristics. Results showed the unique viromic profile with Cirlivirales and Petitvirales as the dominant viruses infecting functional bacteria hosts. The auxiliary metabolic genes (AMGs) focused on element cycles, including metabolisms of carbon (fadA), nitrogen (glnA), sulfur (mddA and cysK) and phosphorus (phoH). Other AMGs were involved in toxic tolerance of hosts, improving their cell membrane and wall robustness, antioxidant, DNA repair and cobalamin biosynthesis. Vice versa, the bloomed host provided fitness advantages for viruses. Dissolved oxygen was found to be the key factor shaping the distributions of viral community and AMGs. Summarizing, the study exposed the mutual virus-bacterium interaction in the AOHO combination providing stable treatment efficiency.

Antibacterial activity and mechanism of X33 antimicrobial oligopeptide against Acinetobacter baumannii

Acinetobacter baumannii is a pathogenic bacterium widespread in human environments, especially in intensive care units, and is associated with high morbidity and infection rates. Multiple drug resistance in A. baumannii frequently leads to the death of patients, making the development of multi-effect antibacterial agents against this bacterium a research hotspot. We have previously found that the X33 antimicrobial oligopeptide can effectively inhibit the growth of Penicillium digitatum and Candida albicans. Herein, we evaluated the antibacterial activity of X33 antimicrobial oligopeptide against A. baumannii by determining the minimum inhibitory concentration, inhibition zone, and growth curve. The increase in extracellular alkaline phosphatase and the leakage of intracellular compounds confirmed the effect of X33 antimicrobial oligopeptide on the cell wall and membrane. Changes in reactive oxygen species, malondialdehyde, ATP, reducing sugar, soluble protein, and pyruvate content demonstrated that the incubation with X33 antimicrobial oligopeptide affected energy metabolism and oxidative stress. Consistent with the physiological characteristics, transcriptomics analysis indicated that incubation with X33 antimicrobial oligopeptide significantly induced changes in the expression of 2339 genes, including 1262 upregulated and 1077 downregulated genes, which participate in oxidative phosphorylation, ribosome, quorum sensing, fatty acid degradation, glycolysis/gluconeogenesis, and citrate cycle pathways. These results provide a fundamental basis for investigating the mechanism of X33 antimicrobial oligopeptide as a potential drug against A. baumannii.

The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans

BACKGROUND

Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the protective role of FldX1 in P. xenovorans LB400 during the degradation of 4-hydroxyphenylacetate (4-HPA) and 3-hydroxyphenylacetate (3-HPA).

METHODS

The functionality of FldX1 was evaluated in P. xenovorans p2-fldX1 that overexpresses FldX1. The effects of FldX1 on P. xenovorans were studied measuring growth on hydroxyphenylacetates, degradation of 4-HPA and 3-HPA, and ROS formation. The effects of hydroxyphenylacetates (HPAs) on the proteome (LC-MS/MS) and gene expression (qRT-PCR) were quantified. Bioaugmentation with strain p2-fldX1 of 4-HPA-polluted soil was assessed, measuring aromatic degradation (HPLC), 4-HPA-degrading bacteria, and plasmid stability.

RESULTS

The exposure of P. xenovorans to 4-HPA increased the formation of ROS compared to 3-HPA or glucose. P. xenovorans p2-fldX1 showed an increased growth on 4-HPA and 3-HPA compared to the control strain WT-p2. Strain p2-fldX1 degraded faster 4-HPA and 3-HPA than strain WT-p2. Both WT-p2 and p2-fldX1 cells grown on 4-HPA displayed more changes in the proteome than cells grown on 3-HPA in comparison to glucose-grown cells. Several enzymes involved in ROS detoxification, including AhpC2, AhpF, AhpD3, KatA, Bcp, CpoF1, Prx1 and Prx2, were upregulated by hydroxyphenylacetates. Downregulation of organic hydroperoxide resistance (Ohr) and DpsA proteins was observed. A downregulation of the genes encoding scavenging enzymes (katE and sodB), and gstA and trxB was observed in p2-fldX1 cells, suggesting that FldX1 prevents the antioxidant response. More than 20 membrane proteins, including porins and transporters, showed changes in expression during the growth of both strains on hydroxyphenylacetates. An increased 4-HPA degradation by recombinant strain p2-fldX1 in soil microcosms was observed. In soil, the strain overexpressing the flavodoxin FldX1 showed a lower plasmid loss, compared to WT-p2 strain, suggesting that FldX1 contributes to bacterial fitness. Overall, these results suggest that recombinant strain p2-fldX1 is an attractive bacterium for its application in bioremediation processes of aromatic compounds.

CONCLUSIONS

The long-chain flavodoxin FldX1 improved the capability of P. xenovorans to degrade 4-HPA in liquid culture and soil microcosms by protecting cells against the degradation-associated oxidative stress.

Isolation, identification, degradation mechanism and exploration of active enzymes in the ochratoxin A degrading strain Acinetobacter pittii AP19

Ochratoxin A (OTA) is a polyketide mycotoxin that commonly contaminates agricultural products and causes significant economic losses. In this study, the efficient OTA-degrading strain AP19 was isolated from vineyard soil and was identified as Acinetobacter pittii. Compared with growth in nutrient broth supplemented with OTA (OTA-NB), strain AP19 grew faster in nutrient broth (NB), but the ability of the resulting cell lysates to remove OTA was weaker. After cultivation in NB, the cell lysate of strain AP19 was able to remove 100% of 1 mg/L OTA within 18 h. The cell lysate fraction > 30 kDa degraded 100% of OTA within 12 h, while the fractions < 30 kDa were practically unable to degrade OTA. Further anion exchange chromatography of the > 30 kDa fraction yielded two peaks exhibiting significant OTA degradation activity. The degradation product was identified as OTα. Amino acid metabolism exhibited major transcriptional trends in the response of AP19 to OTA. The dacC gene encoding carboxypeptidase was identified as one of the contributors to OTA degradation. Soil samples inoculated with strain AP19 showed significant OTA degradation. These results provide significant insights into the discovery of novel functions in A. pittii, as well as its potential as an OTA decomposer.

Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil

Tracking the metabolic activity of whole soil communities can improve our understanding of the transformation and fate of carbon in soils. We used stable isotope metabolomics to trace 13C from nine labeled carbon sources into the water-soluble metabolite pool of an agricultural soil over time. Soil was amended with a mixture of all nine sources, with one source isotopically labeled in each treatment. We compared changes in the 13C enrichment of metabolites with respect to carbon source and time over a 48-day incubation and contrasted differences between soluble sources (glucose, xylose, amino acids, etc.) and insoluble sources (cellulose and palmitic acid). Whole soil metabolite profiles varied singularly by time, while the composition of 13C-labeled metabolites differed primarily by carbon source (R2 = 0.68) rather than time (R2 = 0.07), with source-specific differences persisting throughout incubations. The 13C labeling of metabolites from insoluble carbon sources occurred slower than that from soluble sources but yielded a higher average atom percent (atom%) 13C in metabolite markers of biomass (amino acids and nucleic acids). The 13C enrichment of metabolite markers of biomass stabilized between 5 and 15 atom% 13C by the end of incubations. Temporal patterns in the 13C enrichment of tricarboxylic acid cycle intermediates, nucleobases (uracil and thymine), and by-products of DNA salvage (allantoin) closely tracked microbial activity. Our results demonstrate that metabolite production in soils is driven by the carbon source supplied to the community and that the fate of carbon in metabolites do not generally converge over time as a result of ongoing microbial processing and recycling. IMPORTANCE Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13C from supplied carbon sources into metabolite pools and biomass. We show that differences in the metabolism of sources influence the fate of carbon in soils. Heterogeneity in 13C-labeled metabolite profiles corresponded with compositional differences in the metabolically active populations, providing a basis for how microbial community composition correlates with the quality of soil carbon. Our study demonstrates the application of SIP-metabolomics in studying soils and identifies several metabolite markers of growth, activity, and other aspects of microbial function.

A study of highly efficient phenol biodegradation by a versatile Bacillus cereus ZWB3 on aerobic condition

As one of the organic pollutants in industrial wastewater, phenol seriously threatens the environment and human health. Among various methods, microbial degradation of phenol possesses the advantages of nontoxicity and no secondary pollution. Therefore, search for microbial resources that can efficiently degrade phenol has become an important issue. In this study, a strain that could efficiently degrade phenol was isolated. The strain was identified as Bacillus cereus based on its morphology, physiological and biochemical features and 16S rRNA sequence analysis. The strain can completely degrade phenol up to 1,500 mg/L within 26 h (57.7 mg·L^-1·h^-1), under the optimum conditions, faster compared with the known degrading bacteria. The strain could efficiently remove phenol at a wide range of temperatures (22-37 °C) and pH (7-9), and Mn²⁺ and Zn²⁺ stress. Interestingly, this strain displayed the potential on microthermal environment, which could degrade 1,200 mg/L phenol within 36 h at 22 °C. Further, the strain had capacity that used a variety of aromatic compounds as the sole carbon source for growth. This study shows a useful biodegradation route on the wastewater treatment under high phenol concentration conditions, providing alternatives for environmental remediation.

Transcriptomic Responses of Mycoplasma bovis Upon Treatments of trans-Cinnamaldehyde, Carvacrol, and Eugenol

Mycoplasma bovis (M. bovis) is an insidious, wall-less primary bacterial pathogen that causes bovine pneumonia, mid-ear infection, mastitis, and arthritis. The economic losses caused by M. bovis due to culling, diminished milk production, and feed conversion are underestimated because of poor diagnosis/recognition. Treatment with common antibiotics targeting the cell wall is ineffective. Plant-derived antimicrobials (PDAs) such as food-grade trans-cinnamaldehyde (TC), eugenol (EU), and carvacrol (CAR) are inexpensive and generally regarded as safe for humans and animals yet possess strong anti-bacterial properties. In preliminary studies, we found that all three PDAs inhibited the growth of M. bovis in vitro. Through RNA sequencing, we report here that CAR affected the expression of 153 genes which included the downregulation of energy generation-related proteins, pentose phosphate pathway, and upregulation of ribosomes and translation-related proteins. Few differentially expressed genes were found when M. bovis was treated with TC, EU, or when the three PDAs were double or triple combined. Our results suggest that, as opposed to the effect of CAR, the growth-inhibitory effects of TC and EU at levels tested may be exerted through mechanisms other than gene expression regulations.

Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1

The continuing reports of plastic pollution in various ecosystems highlight the threat posed by the ever-increasing consumption of synthetic polymers. Therefore, Pseudomonas capeferrum TDA1, a strain recently isolated from a plastic dump site, was examined further regarding its ability to degrade polyurethane (PU) compounds. The previously reported degradation pathway for 2,4-toluene diamine, a precursor and degradation intermediate of PU, could be confirmed by RNA-seq in this organism. In addition, different cell fractions of cells grown on a PU oligomer were tested for extracellular hydrolytic activity using a standard assay. Strikingly, purified outer membrane vesicles (OMV) of P. capeferrum TDA1 grown on a PU oligomer showed higher esterase activity than cell pellets. Hydrolases in the OMV fraction possibly involved in extracellular PU degradation were identified by mass spectrometry. On this basis, we propose a model for extracellular degradation of polyester-based PUs by P. capeferrum TDA1 involving the role of OMVs in synthetic polymer degradation.

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.

Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment

Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the “seed” bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.

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.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.

Acinetobacter calcoaceticus CSY-P13 Mitigates Stress of Ferulic and p-Hydroxybenzoic Acids in Cucumber by Affecting Antioxidant Enzyme Activity and Soil Bacterial Community

Ferulic acid (FA) and p-hydroxybenzoic acid (PHBA) are main phenolic compounds accumulated in rhizosphere of continuously cropped cucumber, causing stress in plants. Microbial degradation of a mixture of FA and PHBA is not well understood in soil. We isolated a strain CSY-P13 of Acinetobacter calcoaceticus, inoculated it into soil to protect cucumber from FA and PHBA stress, and explored a mechanism underlying the protection. CSY-P13 effectively degraded a mixture of FA and PHBA in culture solution under conditions of 39.37°C, pH 6.97, and 21.59 g L-1 potassium dihydrogen phosphate, giving rise to 4-vinyl guaiacol, vanillin, vanillic acid, and protocatechuic acid. During FA and PHBA degradation, activities of superoxide dismutase (SOD), catalase, ascorbate peroxidase, and dehydroascorbate reductase in CSY-P13 were induced. Inoculated into cucumber-planted soil containing 220 μg g-1 mixture of FA and PHBA, CSY-P13 degraded FA and PHBA in soil, increased plant height, and decreased malonaldehyde, superoxide radical, and hydrogen peroxide levels in leaves. CSY-P13 also enhanced SOD, guaiacol peroxidase, catalase, glutathione peroxidase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase activities; increased ascorbate and glutathione contents; and elevated transcript levels of copper/zinc SOD, manganese SOD, and catalase in leaves under FA and PHBA. Moreover, CSY-P13 increased phosphatase, catalase, urease, and sucrase activities and changed bacterial richness, diversity, and community composition by high throughput sequencing in cucumber-planted soil supplemented with the mixture of FA and PHBA. So CSY-P13 degrades the mixture of FA and PHBA in soil and mitigates stress from the two phenolic compounds in cucumber by activating antioxidant enzymes, changing soil bacterial community, and inducing soil enzymes.

Effects of phenol on sulfate reduction by mixed microbial culture: kinetics and bio-kinetics analysis

Mixed microbial culture collected from the wastewater treatment plant of Indian Institute of Technology Guwahati (IITG) was further grown in anaerobic condition in presence of sulfate where lactate was added as a carbon source. Sulfate addition was increased stepwise up to 1,000 mg l^-1 before phenol was added at increasing concentrations from 10 mg l^-1 to 300 mg l^-1. Kinetics of sulfate, phenol and chemical oxygen demand reduction were studied and experimental findings were analyzed using various bio-models to estimate the bio-kinetic coefficients. This is the first detailed report on kinetics and bio-kinetic studies of sulfate reduction in presence of phenol. Experimental results showed that there was no inhibition of sulfate reduction and microbial growth up to 100 mg l^-1 phenol addition. However, inhibition to different degrees was observed at higher phenol addition. The experimental data of microbial growth and substrate consumption in presence of phenol fitted well to the Edward model (R² = 0.85, root mean square error = 0.001011) with maximum specific growth rate = 0.052 h^-1, substrate inhibition constant = 88.05 mg l^-1 and half saturation constant = 58.22 mg l^-1. The characteristics of the cultured microbes were determined through a series of analysis and microbial tests.