Real-time PCR based analysis of metal resistance genes in metal resistant Pseudomonas aeruginosa strain J007

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

BACKGROUND

The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance.

RESULTS

The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data.

CONCLUSIONS

Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Controlling AMR in the Pig Industry: Is It Enough to Restrict Heavy Metals?

Heavy metals have the potential to influence the transmission of antimicrobial resistance (AMR). However, the effect on AMR caused by heavy metals has not been clearly revealed. In this study, we used a microcosm experiment and metagenomics to examine whether common levels of Cu and Zn in pig manure influence AMR transmission in manured soil. We found that the abundance of 204 ARGs significantly increased after manure application, even though the manure did not contain antibiotic residuals. However, the combined addition of low Cu and Zn (500 and 1000 mg/kg, respectively) only caused 14 ARGs to significantly increase, and high Cu and Zn (1000 and 3000 mg/kg, respectively) caused 27 ARGs to significantly increase. The disparity of these numbers suggested that factors within the manure were the primary driving reasons for AMR transmission, rather than metal amendments. A similar trend was found for biocide and metal resistance genes (BMRGs) and mobile genetic elements (MGEs). This study offers deeper insights into AMR transmission in relation to the effects of manure application and heavy metals at commonly reported levels. Our findings recommend that more comprehensive measures in controlling AMR in the pig industry are needed apart from restricting heavy metal additions.

Cu and Zn exert a greater influence on antibiotic resistance and its transfer than doxycycline in agricultural soils

Livestock manure is a main source of heavy metals, antibiotics and antibiotic resistance genes (ARGs) in agricultural soils. The co-existence of heavy metals and ARGs needs to be systematically studied, since manure application is greatly encouraged. In this study, we examined soils for alterations in antibiotic resistance where doxycycline, Cu, and Zn were added equivalent to those found in typical pig manure applications. The results indicated that high levels of Cu inhibited soil respiration and urease for the first 10 days. Metagenomic analysis demonstrated that Cu and Zn additions caused profound alterations in bacterial community, metal resistance genes (MRGs) and mobile genetic elements. Among the differential ARGs, efflux pump genes took a significantly high ratio compared with control for the first 5 days, emphasizing their important roles in the profile of antibiotic resistance. Moreover, the number of differential MRGs was < 30 for doxycycline treatment, but 66-87 for Cu and Zn treatments. The number of differential integrative and conjugative elements was 3 for doxycycline treatment, and 6-13 for Cu and Zn treatments. Overall, high Cu and Zn levels caused a greater influence than did doxycycline on bacterial communities and transfer of antibiotic resistance in soil.

Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source

Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.

Characterization of the copper resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain isolated from copper mine sludge

Bioremediation is one of the most effective ways for removal of heavy metals and restoration of contaminated sites. This study investigated the copper (Cu) resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain KW3 isolated from sludge of Cu mine. The effect of Cu concentrations on the bacterial growth, biomass, and adsorption capacity, as well as the effect of contact time on the adsorption process was evaluated in a batch biosorption test. The strain exhibited strong tolerance of Cu, and the minimal inhibitory concentration was around 400 mg Cu²⁺ L^-1, at which the maximum adsorption capacity was 14.1 mg g^-1 dry cell mass. Cell walls and intracellular soluble components adsorbed 51.2% and 46.6% of Cu²⁺, respectively, suggesting that the strain not only adsorbed Cu²⁺ on the surface but also metastasized ions into cells. The adsorption and kinetic data were well fitted with Freundlich isotherm and Pseudo-second-order models, suggesting that cell surface had a high affinity for Cu²⁺ and the chemisorption could be the main adsorption mechanism. Scanning electron microscope and Fourier transform infrared spectroscopy analysis revealed that hydroxyl, carboxylic, amide, sulfate, and phosphate on cell walls might be involved in the biosorption process. Two-dimensional gel electrophoresis and MALDI-TOF/TOF mass spectrometry revealed that some oxidoreductases, in particular Cu resistance protein A (CopA) expression levels, were upregulated. Antioxidant defense and P_1B-type ATPases CopA efflux might play a crucial role in maintaining cellular homeostasis and intracellular detoxification. To our knowledge, this is the first time that Cu resistance mechanisms, especially intracellular enzymatic mechanisms, were identified in an A. calcoaceticus KW3 strain.

The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp) sequences tentatively assigned to CzcA family heavy metal efflux pump [YP_001899332] from Ralstonia picketii 12J with 99% similarity. In this study the bacterium MR-CH-I2 and its heavy-metal resistance determinant were more precisely identified. This bacterial isolate was on the base of phylogenetic analysis of almost the whole (1,500 bp) 16S rDNA (16S rRNA) sequence, MR-CH-I2 [MF102046], and sequence for gyrB gene and its product respectively, MR-CH-I2-gyrB [MF134666], assigned to R. picketii 12J [CP001068] with 99 and 100% similarities, respectively. In addition, the whole nccA-like heavy-metal resistance gene sequence (3,192 bp), marked as MR-CH-I2-nccA [KR476581], was obtained and on the base of phylogenetic analysis its assignment was confirmed to MULTISPECIES: cation efflux system protein CzcA [WP_004635342] from Burkholderiaceae with 98% similarity. Furthermore, although the bacterium carried one high molecular plasmid of about 50 kb in size, nccA-like gene was not located on this plasmid. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.

Characterization of arsenic oxidation and uranium bioremediation potential of arsenic resistant bacteria isolated from uranium ore

Arsenic (As) is often found naturally as the co-contaminant in the uranium (U)-contaminated area, obstructing the bioremediation process. Although the U-contaminated environment harbors microorganisms capable of interacting with U which could be exploited in bioremediation. However, they might be unable to perform with their full potential due to As toxicity. Therefore, potential in arsenic resistance and oxidation is greatly desired among the microorganisms for a continued bioremediation process. In this study, arsenic-resistant bacteria were isolated from U ore collected from Bundugurang U mine, characterized and their As oxidation and U removal potentials were determined. 16S rRNA gene sequencing and phylogenetic analysis showed the affiliation of isolated bacteria with Microbacterium, Micrococcus, Shinella, and Bacillus. Except Bacillus sp. EIKU7, Microbacterium sp. EIKU5, Shinella sp. EIKU6, and Micrococcus sp. EIKU8 were found to resist more than 400 mM As(V); however, all the isolates could survive in 8 mM As(III). The isolates were found to readily oxidize As under different culture conditions and are also resistant towards Cd, Cr, Co, Ni, and Zn. All the isolates could remove more than 350 mg U/g dry cells within 48 h which were found to be highly dependent upon the concentration of U, biomass added initially, and on the time of exposure. Ability of the isolates to grow in nitrogen-free medium indicated that they can flourish in the nutrition deprived environment. Therefore, the recovery of isolates with the potent ability to resist and oxidize As from U ore might play an important role in toxic metal bioremediation including U.

Proteome profiling of Pseudomonas aeruginosa PAO1 identifies novel responders to copper stress

BACKGROUND

The opportunistic pathogen, Pseudomonas aeruginosa is well known for its environmental and metabolic versatility, yet many of the functions of its gene-products remain to be fully elucidated. This study's objective was to illuminate the potential functions of under-described gene-products during the medically relevant copper-stress condition.

RESULTS

We used data-independent acquisition mass spectrometry to quantitate protein expression changes associated with copper stress in P. aeruginosa PAO1. Approximately 2000 non-redundant proteins were quantified, with 78 proteins altering in abundance by +/- 1.5-fold or more when cultured to mid-log growth in the presence of 50 μM copper sulfate. One-third of those differentially expressed proteins have no prior established functional roles.

CONCLUSIONS

This study provides evidence for the functional involvement of some specific proteins in enabling P. aeruginosa to survive under sub-lethal concentrations of copper. This further paves the way for targeted investigations into the specific mechanisms of their activity.

Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance

Pseudomonas sp. QTF5 was isolated from the continuous permafrost near the bitumen layers in the Qiangtang basin of Qinghai-Tibetan Plateau in China (5,111 m above sea level). It is psychrotolerant and highly and widely tolerant to heavy metals and has the ability to metabolize benzoic acid and salicylic acid. To gain insight into the genetic basis for its adaptation, we performed whole genome sequencing and analyzed the resistant genes and metabolic pathways. Based on 120 published and annotated genomes representing 31 species in the genus Pseudomonas, in silico genomic DNA-DNA hybridization (<54%) and average nucleotide identity calculation (<94%) revealed that QTF5 is closest to Pseudomonas lini and should be classified into a novel species. This study provides the genetic basis to identify the genes linked to its specific mechanisms for adaptation to extreme environment and application of this microorganism in environmental conservation.

Efflux drug transporters at the forefront of antimicrobial resistance

Bacterial antibiotic resistance is rapidly becoming a major world health consideration. To combat antibiotics, microorganisms employ their pre-existing defence mechanisms that existed long before man’s discovery of antibiotics. Bacteria utilise levels of protection that range from gene upregulation, mutations, adaptive resistance, and production of resistant phenotypes (persisters) to communal behaviour, as in swarming and the ultimate defence of a biofilm. A major part of all of these responses involves the use of antibiotic efflux transporters. At the single cell level, it is becoming apparent that the use of efflux pumps is the first line of defence against an antibiotic, as these pumps decrease the intracellular level of antibiotic while the cell activates the various other levels of protection. This frontline of defence involves a coordinated network of efflux transporters. In the future, inhibition of this efflux transporter network, as a target for novel antibiotic therapy, will require the isolation and then biochemical/biophysical characterisation of each pump against all known and new antibiotics. This depth of knowledge is required so that we can fully understand and tackle the mechanisms of developing antimicrobial resistance.