Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes

A flow equilibrium of zinc in cells of Cupriavidus metallidurans

The hypothesis was tested that a kinetical flow equilibrium of uptake and efflux reactions is responsible for balancing the cellular zinc content. The experiments were done with the metal-resistant bacterium Cupriavidus metallidurans. In pulse-chase experiments, the cells were loaded with radioactive 65Zn and chased with the 100-fold concentration of non-radioactive zinc chloride. In parallel, the cells were loaded with isotope-enriched stable 67Zn and chased with non-enriched zinc to differentiate between zinc pools in the cell. The experiments demonstrated the existence of a kinetical flow equilibrium, resulting in a constant turnover of cell-bound zinc ions. The absence of the metal-binding cytoplasmic components, polyphosphate and glutathione, metal uptake, and metal efflux systems influenced the flow equilibrium. The experiments also revealed that not all zinc uptake and efflux systems are known in C. metallidurans. Cultivation of the cells under zinc-replete, zinc-, and zinc-magnesium-starvation conditions influenced zinc import and export rates. Here, magnesium starvation had a stronger influence compared to zinc starvation. Other metal cations, especially cobalt, affected the cellular zinc pools and zinc export during the chase reaction. In summary, the experiments with 65Zn and 67Zn demonstrated a constant turnover of cell-bound zinc. This indicated that simultaneously occurring import and export reactions in combination with cytoplasmic metal-binding components resulted in a kinetical flow equilibrium that was responsible for the adjustment of the cellular zinc content.

IMPORTANCE

Understanding the biochemical action of a single enzyme or transport protein is the pre-requisite to obtain insight into its cellular function but this is only one half of the coin. The other side concerns the question of how central metabolic functions of a cell emerge from the interplay of different proteins and other macromolecules. This paper demonstrates that a flow equilibrium of zinc uptake and efflux reactions is at the core of cellular zinc homeostasis and identifies the most important contributors to this flow equilibrium: the uptake and efflux systems and metal-binding components of the cytoplasm.

In a state of flux: new insight into the transport processes that maintain bacterial metal homeostasis

A new study by Nies et al. (J Bacteriol 206:e00080-24, 2024, https://doi.org/10.1128/jb.00080-24) provides a rich, quantitative data set of zinc accumulation by cells of Cupriavidus metallidurans, including of mutant bacterial strains lacking import or efflux genes, and comparison of zinc accumulation by cells previously starved of metal with those of zinc-replete cells. The data surprisingly demonstrate the concomitant activity of both active metal import and metal efflux systems. They present a flow equilibrium model to describe zinc homeostasis in bacteria.

Screening of heavy metal-resistant rhizobial and non-rhizobial microflora isolated from Trifolium sp. growing in mining areas

Plant growth-promoting rhizobacteria (PGPR) can promote plant growth and development with several beneficial effects, especially in challenging environmental conditions, such as the presence of toxic contaminants. In this study, 49 isolates obtained from Trifolium sp. nodules growing on a Pb/Zn mine site were characterized for PGP traits including siderophores production, phosphate solubilization, extracellular enzymes production, and antifungal activity. The isolates were also screened for their ability to grow at increasing concentrations of NaCl and heavy metals, including lead, zinc, cobalt, copper, nickel, cadmium, and chromium. The findings of our study indicated that isolates Cupriavidus paucula RSCup01-RSCup08, Providencia rettgeri RSPro01, Pseudomonas putida RSPs01, Pseudomonas thivervalensis RSPs03-RSPs09, and Acinetobacter beijerinckii RSAci01 showed several key traits crucial for promoting plant growth, thus demonstrating the greatest potential. Most isolates displayed resistance to salt and heavy metals. Notably, Staphylococcus xylosus RSSta01, Pseudomonas sp. RSPs02, Micrococcus yunnanensis RSMicc01, and Kocuria dechangensis RSKoc01 demonstrated a significant capacity to grow at salt concentrations ranging from 10 to 20%, and isolates including Cupravidus paucula RSCup01-RSCup08 exhibited resistance to high levels of heavy metals, up to 1300 mg/L Pb++, 1200 mg/L Zn++, 1000 mg/L Ni++, 1000 mg/L Cd++, 500 mg/L Cu++, 400 mg/L Co++, and 50 mg/L CrVI+. Additionally, the analysis revealed that metal-resistant genes pbrA, czcD, and nccA were exclusively detected in the Cupriavidus paucula RSCup01 strain. The results of this study provide insights into the potential of plant growth-promoting rhizobacteria strains that might be used as inoculants to improve phytoremediation in heavy metal-contaminated soils.

The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria

Many bacteria have the ability to survive in challenging environments; however, they cannot all grow on standard culture media, a phenomenon known as the viable but non-culturable (VBNC) state. Bacteria commonly enter the VBNC state under nutrient-poor environments or under stressful conditions. This review explores the concept of the VBNC state, providing insights into the beneficial bacteria known to employ this strategy. The investigation covers different chemical and physical factors that can induce the latency state, cell features, and gene expression observed in cells in the VBNC state. The review also covers the significance and applications of beneficial bacteria, methods of evaluating bacterial viability, the ability of bacteria to persist in environments associated with higher organisms, and the factors that facilitate the return to the culturable state. Knowledge about beneficial bacteria capable of entering the VBNC state remains limited; however, beneficial bacteria in this state could face adverse environmental conditions and return to a culturable state when the conditions become suitable and continue to exert their beneficial effects. Likewise, this unique feature positions them as potential candidates for healthcare applications, such as the use of probiotic bacteria to enhance human health, applications in industrial microbiology for the production of prebiotics and functional foods, and in the beer and wine industry. Moreover, their use in formulations to increase crop yields and for bacterial bioremediation offers an alternative pathway to harness their beneficial attributes.

Stimulation the immune response through ξ potential on core-shell 'calcium oxide/magnetite iron oxides' nanoparticles

This study investigated the role of ξ Potential on Monometallic (MM) and Bimetallic (BM) Calcium Oxide/Magnetite Iron Oxides nanoparticles to stimulate the immune response. Metallic nanoparticles (MNPs) were biosynthesis using Pseudomonas fluorescens S48. MNPs characterization was carried out by UV-Vis spectra, XRD analysis, Zeta potential and Particles size, SEM-EDS, and TEM, and the concentrations were calculated by ICP-AES. The immune system activity was measured by estimation of lymphocytes transformation, phagocytic activity. The end point was in evaluating the toxicity of Metallic NPs by comet assay. SEM-EDS and TEM micrographs showed that MM CaO and Fe3O4 represent a perfect example of zero-dimensional (0-D) NPs with cubic and spherical particles in shape, while BM CaO/Fe3O4 NPs appeared in the form of Core-shell structure. The variations effect of novelty MM, BM CaO/Fe3O4 NPs in enhancing immune activity were based on the ξ Potential whereas negatively and positively charged. These findings demonstrate that the cationic CaO/Fe3O4 NPs are inefficient in stimulating the immune system which causes a high cytotoxic effect. But the anionic CaO/Fe3O4 NPs have advantages in targeting the immune system because of enhanced delivery to the cells through adsorptive endocytosis as well as the half-life clearance from the blood.

Biofilm-a Syntrophic Consortia of Microbial Cells: Boon or Bane?

Biofilm is the conglomeration of microbial cells which is associated with a surface. In the recent times, the study of biofilm has gained popularity and vivid research is being done to know about the effects of biofilm and that it consists of many organisms which are symbiotic in nature, some of which are human pathogens. Here, in this study, we have discussed about biofilms, its formation, relevance of its presence in the biosphere, and the possible remediations to cope up with its negative effects. Since removal of biofilm is difficult, emphasis has been made to suggest ways to prevent biofilm formation and also to devise ways to utilize biofilm in an economically and environment-friendly method.

Quantitative Proteomic Analysis of Cyanide and Mercury Detoxification by Pseudomonas pseudoalcaligenes CECT 5344

The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT 5344 uses cyanide and different metal-cyanide complexes as the sole nitrogen source. Under cyanotrophic conditions, this strain was able to grow with up to 100 μM mercury, which was accumulated intracellularly. A quantitative proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been applied to unravel the molecular basis of the detoxification of both cyanide and mercury by the strain CECT 5344, highlighting the relevance of the cyanide-insensitive alternative oxidase CioAB and the nitrilase NitC in the tolerance and assimilation of cyanide, independently of the presence or absence of mercury. Proteins overrepresented in the presence of cyanide and mercury included mercury transporters, mercuric reductase MerA, transcriptional regulator MerD, arsenate reductase and arsenical resistance proteins, thioredoxin reductase, glutathione S-transferase, proteins related to aliphatic sulfonates metabolism and sulfate transport, hemin import transporter, and phosphate starvation induced protein PhoH, among others. A transcriptional study revealed that from the six putative merR genes present in the genome of the strain CECT 5344 that could be involved in the regulation of mercury resistance/detoxification, only the merR2 gene was significantly induced by mercury under cyanotrophic conditions. A bioinformatic analysis allowed the identification of putative MerR2 binding sites in the promoter regions of the regulatory genes merR5, merR6, arsR, and phoR, and also upstream from the structural genes encoding glutathione S-transferase (fosA and yghU), dithiol oxidoreductase (dsbA), metal resistance chaperone (cpxP), and amino acid/peptide extruder involved in quorum sensing (virD), among others. IMPORTANCE Cyanide, mercury, and arsenic are considered very toxic chemicals that are present in nature as cocontaminants in the liquid residues generated by different industrial activities like mining. Considering the huge amounts of toxic cyanide- and mercury-containing wastes generated at a large scale and the high biotechnological potential of P. pseudoalcaligenes CECT 5344 in the detoxification of cyanide present in these industrial wastes, in this work, proteomic, transcriptional, and bioinformatic approaches were used to characterize the molecular response of this bacterium to cyanide and mercury, highlighting the mechanisms involved in the simultaneous detoxification of both compounds. The results generated could be applied for developing bioremediation strategies to detoxify wastes cocontaminated with cyanide, mercury, and arsenic, such as those generated at a large scale in the mining industry.

Effects of dissolved organic matter derived from cow manure on heavy metal(loid)s and bacterial community dynamics in mercury-thallium mining waste slag

Organic amendments in aided phytostabilization of waste slag containing high levels of heavy metal (loid)s (HMs) are an important way to control the release of HMs in situ. However, the effects of dissolved organic matter (DOM) derived from organic amendments on HMs and microbial community dynamics in waste slag are still unclear. Here, the effect of DOM derived from organic amendments (cow manure) on the geochemical behaviour of HMs and the bacterial community dynamics in mercury (Hg)-thallium (Tl) mining waste slag were investigated. The results showed that the Hg-Tl mining waste slag without the addition of DOM continuously decreased the pH and increased the EC, Eh, SO42-, Hg, and Tl levels in the leachate with increasing incubation time. The addition of DOM significantly increased the pH, EC, SO42-, and arsenic (As) levels but decreased the Eh, Hg, and Tl levels. The addition of DOM significantly increased the diversity and richness of the bacterial community. The dominant bacterial phyla (Proteobacteria, Firmicutes, Acidobacteriota, Actinobacteriota, and Bacteroidota) and genera (Bacillus, Acinetobacter, Delftia, Sphingomonas, and Enterobacter) were changed in association with increases in DOM content and incubation time. The DOM components in the leachate were humic-like substances (C1 and C2), and the DOC content and maximum fluorescence intensity (FMax) values of C1 and C2 in the leachate decreased and first increased and then decreased with increasing incubation time. The correlations between HMs and DOM and the bacterial community showed that the geochemical behaviours of HMs in Hg-Tl mining waste slag were directly influenced by DOM-mediated properties and indirectly influenced by DOM regulation of bacterial community changes. Overall, these results indicated that DOM properties associated with bacterial community changes increased As mobilization but decreased Hg and Tl mobilization from Hg-Tl mining waste slag.

Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies

The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.

Characterization and Association of Rips Repertoire to Host Range of Novel Ralstonia solanacearum Strains by In Silico Approaches

Ralstonia solanacearum species complex (RSSC) cause several phytobacteriosis in many economically important crops around the globe, especially in the tropics. In Brazil, phylotypes I and II cause bacterial wilt (BW) and are indistinguishable by classical microbiological and phytopathological methods, while Moko disease is caused only by phylotype II strains. Type III effectors of RSSC (Rips) are key molecular actors regarding pathogenesis and are associated with specificity to some hosts. In this study, we sequenced and characterized 14 newly RSSC isolates from Brazil's Northern and Northeastern regions, including BW and Moko ecotypes. Virulence and resistance sequences were annotated, and the Rips repertoire was predicted. Confirming previous studies, RSSC pangenome is open as α≅0.77. Genomic information regarding these isolates matches those for R. solanacearum in NCBI. All of them fit in phylotype II with a similarity above 96%, with five isolates in phylotype IIB and nine in phylotype IIA. Almost all R. solanacearum genomes in NCBI are actually from other species in RSSC. Rips repertoire of Moko IIB was more homogeneous, except for isolate B4, which presented ten non-shared Rips. Rips repertoire of phylotype IIA was more diverse in both Moko and BW, with 43 common shared Rips among all 14 isolates. New BW isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. Rips not shared with other isolates might contribute to individual virulence, but commonly shared Rips are good avirulence candidates. The high number of Rips shared by new Moko and BW isolates suggests they are actually Moko isolates infecting solanaceous hosts. Finally, infection assays and Rips expression on different hosts are needed to better elucidate the association between Rips repertoire and host specificities.

Mechanism of lead adsorption by a Bacillus cereus strain with indole-3-acetic acid secretion and inorganic phosphorus dissolution functions

BACKGROUND

Heavy metal pollution has become a major source of environmental pollution because of increasing industrialization. Microbial remediation is a promising approach to remediate lead-contaminated environments owing to its cost-effective, environment-friendly, ecologically sustainable, and highly efficient properties. In this study, the growth-promoting functions and lead-adsorption ability of Bacillus cereus SEM-15 were examined, and the functional mechanism of the strain was preliminarily identified using scanning electron microscopy, energy spectrum, infrared spectrum, and genome analyses, providing theoretical support for utilization of B. cereus SEM-15 in heavy metals remediation.

RESULTS

B. cereus SEM-15 showed strong ability to dissolve inorganic phosphorus and secrete indole-3-acetic acid. The lead adsorption efficiency of the strain at lead ion concentration of 150 mg/L was more than 93%. Single factor analysis revealed the optimal conditions for heavy metal adsorption by B. cereus SEM-15 (adsorption time, initial lead ion concentration, pH, and inoculum amount were 10 min, 50-150 mg/L, 6-7, and 5 g/L, respectively) in nutrient-free environment, with the lead adsorption rate reaching 96.58%. Scanning electron microscopy of B. cereus SEM-15 cells before and after lead adsorption showed adherence of a large number of granular precipitates to the cell surface after lead adsorption. X-Ray photoelectron spectroscopy and Fourier transform infrared spectroscopy results indicated the characteristic peaks of Pb-O, Pb-O-R (R = functional group), and Pb-S bonds after lead adsorption, and a shift in the characteristic peaks of bonds and groups related to C, N, and O. Genome annotation results showed the presence of genes related to heavy metals tolerance and plant growth promotion in B. cereus SEM-15, providing a molecular basis for the strain's heavy metals tolerance and plant growth promotion functions.

CONCLUSIONS

This study analyzed the lead adsorption characteristics of B. cereus SEM-15 and the associated influencing factors, and discussed the adsorption mechanism and related functional genes, providing a basis for clarifying the underlying molecular mechanism and offering a reference for further research on plant-microorganisms combined remediation of heavy metals polluted environments.

Identification and Characterization of a Au(III) Reductase from Erwinia sp. IMH

Microorganisms contribute to the formation of secondary gold (Au) deposits through enzymatic reduction of Au(III) to Au(0). However, the enzyme that catalyzes the reduction of Au(III) remains enigmatic. Here, we identified and characterized a previously unknown Au reductase (GolR) in the cytoplasm of Erwinia sp. IMH. The expression of golR was strongly up-regulated in response to increasing Au(III) concentrations and exposure time. Mutant with in-frame deletion of golR was incapable of reducing Au(III), and the capability was rescued by reintroducing wild-type golR into the mutant strain. The Au(III) reduction was determined to occur in the cytoplasmic space by comparing the TEM images of the wild-type, mutant, and complemented strains. In vitro assays of the purified GolR protein confirmed its ability to reduce Au(III) to Au nanoparticles. Molecular dynamic simulations demonstrated that the hydrophobic cavity of GolR may selectively bind AuCl₂(OH)₂ ^-, the predominant auric chloride species at neutral pH. Density functional theory calculations revealed that AuCl₂(OH)₂ ^- may be coordinated at the Fe-containing active site of GolR and is probably reduced via three consecutive proton-coupled electron transfer processes. The new class of reductase, GolR, opens the chapter for the mechanistic understanding of Au(III) bioreduction.

Employing gene chip technology for monitoring and assessing soil heavy metal pollution

Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.

A rapid change in microbial communities of the shale gas drilling fluid from 3548 m depth to the above-ground storage tank

Despite the growing body of studies on the various fracturing phrases, the research on the differences between subterranean and surface microorganisms at shale gas drilling sites is still limited. Generally, shale gas development and the production process are divided into drilling and fracturing. The distribution of microbial communities in the latter has been paid some attention, but a deficit remains in terms of our understanding of the microbial community in the former, especially for the phase of drilling flowback and drilling flowback surface. In this study, four drilling flowback fluids (DFFs) (H230-flowback drilling cuttings, H23G-flowback drilling mud, H240-flowback drilling sediment, and H21F-flowback drilling water) from the outlet of subterranean pipeline to the inlet of storage tank were successively collected from H2 shale gas field during its initial drilling in Sichuan, China. Natural mountain water (H10W) used as the injection water of H2 was also sampled. Illumina MiSeq 16S rRNA gene sequencing revealed a total of 8 phyla, 17 classes, 36 orders, 62 families, and 98 genera that were recovered from these samples with uneven distribution. The majority of the obtained sequences belonged to the phyla Proteobacteria (75.36%), Bacteroidetes (10.75%), and Firmicutes (5.64%), with significant differences found in DFFs and injection water. The richness of microorganisms gradually increased with the increasing flowback flowing distance (H230 < H23G < H240 < H21F < H10W), which was employed to reveal a rapid change in microbiota that was evident in samples along the flow path aboveground from a depth of 3548 m. The findings of this study could expand our understanding of the ecological role of microorganisms during the shale gas drilling phase. Furthermore, the study highlights the temporal-spatial trajectory of microbial communities from subterranean environments to the surface in a short period of 30 days.

Identification of a novel heavy metal resistant Ralstonia strain and its growth response to cadmium exposure

A novel Ralstonia Bcul-1 strain was isolated from soil samples that was closest to Ralstonia pickettii. Broad-spectrum resistance was identified to a group of heavy metal ions and tolerance to concentrations of Cd²⁺ up to 400 mg L^-1. Low concentrations of heavy metal ions did not have distinctive impact on heavy metal resistance genes and appeared to induce greater expression. Under exposure to Cd²⁺, cell wall components were significantly enhanced, and some proteins were also simultaneously expressed allowing the bacteria to adapt to the high Cd²⁺ living environment. The maximum removal rate of Cd²⁺ by the Ralstonia Bcul-1 strain was 78.97% in the culture medium supplemented with 100 mg L^-1 Cd²⁺. Ralstonia Bcul-1 was able to survive and grow in a low nutrient and cadmium contaminated (0.42 mg kg^-1) vegetable soil, and the cadmium removal rate was up to 65.76% in 9th growth. Ralstonia Bcul-1 mixed with biochar could maintain sustainable growth of this strain in the soil up to 75 d and the adsorption efficiency of cadmium increased by 16.23-40.80% as compared to biochar application alone. Results from this work suggests that Ralstonia Bcul-1 is an ideal candidate for bioremediation of nutrient deficient heavy metal contaminated soil.

Chromium pollution and its bioremediation mechanisms in bacteria: A review

Environment pollution is at its peak and is creating havoc for living beings. Industrial wastes containing toxic pollutants have contributed to a great extent in this disastrous environment pollution. Chromium (Cr³⁺/Cr⁶⁺) is highly toxic and one of the most common environmental pollutants because of its extensive use in industries especially tanneries. Lack of efficient treatment methods has resulted in extensive chromium pollution. Bioremediation of chromium using bacteria is very thoughtful due to its eco-friendly and cost-effective outcome. Bacteria possess numerous mechanisms such as biosorption, reduction, efflux or bioaccumulation, naturally or acquired to counter the toxicity of chromium. This review focuses on the bacterial responses against chromium toxicity and scope for their application in bioremediation. The differences and similarities between Gram negative and positive bacteria against chromium are also highlighted. Further, the knowledge gap and future prospects are also discussed in order to fill these gaps and overcome the problem associated with real-time applicability of bacterial bioremediation.

The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper

Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.

Lichens-A Potential Source for Nanoparticles Fabrication: A Review on Nanoparticles Biosynthesis and Their Prospective Applications

Green synthesis of nanoparticles (NPs) is a safe, eco-friendly, and relatively inexpensive alternative to conventional routes of NPs production. These methods require natural resources such as cyanobacteria, algae, plants, fungi, lichens, and naturally extracted biomolecules such as pigments, vitamins, polysaccharides, proteins, and enzymes to reduce bulk materials (the target metal salts) into a nanoscale product. Synthesis of nanomaterials (NMs) using lichen extracts is a promising eco-friendly, simple, low-cost biological synthesis process. Lichens are groups of organisms including multiple types of fungi and algae that live in symbiosis. Until now, the fabrication of NPs using lichens has remained largely unexplored, although the role of lichens as natural factories for synthesizing NPs has been reported. Lichens have a potential reducible activity to fabricate different types of NMs, including metal and metal oxide NPs and bimetallic alloys and nanocomposites. These NPs exhibit promising catalytic and antidiabetic, antioxidant, and antimicrobial activities. To the best of our knowledge, this review provides, for the first time, an overview of the main published studies concerning the use of lichen for nanofabrication and the applications of these NMs in different sectors. Moreover, the possible mechanisms of biosynthesis are discussed, together with the various optimization factors influencing the biological synthesis and toxicity of NPs.

Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C

The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.

Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter

Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34^ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterization of CH34^ZnR revealed that it was also more resistant to cadmium, and that it incurred seven insertion sequence-mediated mutations. Among these, an IS1088 disruption of the glpR gene (encoding a DeoR-type transcriptional repressor) resulted in the constitutive expression of the neighboring ATP-binding cassette (ABC)-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34^ZnR with the parental glpR gene further demonstrated that loss of GlpR function and concomitant derepression of the adjacent ABC transporter is pivotal for the observed resistance phenotype. Importantly, addition of glycerol, presumably by glycerol-mediated attenuation of GlpR activity, also promoted increased zinc and cadmium resistance in the parental CH34 strain. Upregulation of this ABC-type transporter is therefore proposed as a new adaptation route towards metal resistance.

Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities

One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.

Integrating biometallurgical recovery of metals with biogenic synthesis of nanoparticles

Industrial activities, such as mining, electroplating, cement production, and metallurgical operations, as well as manufacturing of plastics, fertilizers, pesticides, batteries, dyes or anticorrosive agents, can cause metal contamination in the surrounding environment. This is an acute problem due to the non-biodegradable nature of metal pollutants, their transformation into toxic and carcinogenic compounds, and bioaccumulation through the food chain. At the same time, platinum group metals and rare earth elements are of strong economic interest and their recovery is incentivized. Microbial interaction with metals or metals-bearing minerals can facilitate metals recovery in the form of nanoparticles. Metal nanoparticles are gaining increasing attention due to their unique characteristics and application as antimicrobial and antibiofilm agents, biocatalysts, in targeted drug delivery, for wastewater treatment, and in water electrolysis. Ideally, metal nanoparticles should be homogenous in shape and size, and not toxic to humans or the environment. Microbial synthesis of nanoparticles represents a safe, and environmentally friendly alternative to chemical and physical methods. In this review article, we mainly focus on metal and metal salts nanoparticles synthesized by various microorganisms, such as bacteria, fungi, microalgae, and yeasts, as well as their advantages in biomedical, health, and environmental applications.

Biological-based methods for the removal of volatile organic compounds (VOCs) and heavy metals

The current scenario of increased population and industrial advancement leads to the spoliation of freshwater and tapper of the quality of water. These results decrease in freshwater bodies near all of the areas. Besides, organic and inorganic compounds discharged from different sources into the available natural water bodies are the cause of pollution. The occurrence of heavy metals in water and volatile organic compounds (VOCs) in the air is responsible for a vast range of negative impacts on the atmosphere and human health. Nonetheless, high uses of heavy metals for human purposes may alter the biochemical and geochemical equilibrium. The major air contaminants which are released into the surroundings known as VOCs are produced through different kinds of sources, such as petrochemical and pharmaceutical industries. VOCs are known to cause various health hazards. VOCs are a pivotal group of chemicals that evaporate readily at room temperature. To get over this problem, biofiltration technology has been evolved for the treatment of heavy metals using biological entities such as plants, algae, fungi, and bacteria. Biofiltration technology is a beneficial and sustainable method for the elimination of toxic pollutants from the aquatic environment. Various types of biological technologies ranging from biotrickling filters to biofilters have been developed and they are cost-effective, simple to fabricate, and easy to perform. A significant advantage of this process is the pollutant that is transformed into biodegradable trashes which can decompose within an average time period, thus yielding no secondary pollutants. The aim of this article is to scrutinize the role of biofiltration in the removal of heavy metals in wastewater and VOCs and also to analyze the recent bioremediation technologies and methods.

Construction of a sensitive and specific lead biosensor using a genetically engineered bacterial system with a luciferase gene reporter controlled by pbr and cadA promoters

Background

A bacterial biosensor refers to genetically engineered bacteria that produce an assessable signal in the presence of a physical or chemical agent in the environment.

Methods

We have designed and evaluated a bacterial biosensor expressing a luciferase reporter gene controlled by pbr and cadA promoters in Cupriavidus metallidurans (previously termed Ralstonia metallidurans) containing the CH34 and pI258 plasmids of Staphylococcus aureus, respectively, and that can be used for the detection of heavy metals. In the present study, we have produced and evaluated biosensor plasmids designated pGL3-luc/pbr biosensor and pGL3-luc/cad biosensor, that were based on the expression of luc+ and under the control of the cad promoter and the cadC gene of S. aureus plasmid pI258 and pbr promoter and pbrR gene from plasmid pMOL30 of Cupriavidus metallidurans.

Results

We found that the pGL3-luc/pbr biosensor may be used to measure lead concentrations between 1–100 μM in the presence of other metals, including zinc, cadmium, tin and nickel. The latter metals did not result in any significant signal. The pGL3-luc/cad biosensor could detect lead concentrations between 10 nM to 10 μM.

Conclusions

This biosensor was found to be specific for measuring lead ions in both environmental and biological samples.

Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals

Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.

The CzcCBA Efflux System Requires the CadA P-Type ATPase for Timely Expression Upon Zinc Excess in Pseudomonas aeruginosa

Zinc (Zn) is a trace element essential for life but can be toxic if present in excess. While cells have import systems to guarantee a vital Zn intracellular concentration, they also rely on export systems to avoid lethal Zn overload. In particular, the opportunistic pathogen Pseudomonas aeruginosa possesses four Zn export systems: CadA, CzcCBA, CzcD, and YiiP. In this work, we compare the importance for bacterial survival of each export system at high Zn concentrations. We show that the P-type ATPase CadA, and the efflux pump CzcCBA are the main efflux systems affecting the bacterium tolerance to Zn. In addition, cadA and czcCBA genes expression kinetics revealed a hierarchical organization and interdependence. In the presence of high Zn concentrations, cadA expression is very rapidly induced (<1 min), while czcCBA expression occurs subsequently (>15 min). Our present data show that the fast responsiveness of cadA to Zn excess is due to its transcriptional activator, CadR, which is constitutively present on its promoter and promptly activating cadA gene expression upon Zn binding. Moreover, we showed that CadA is essential for a timely induction of the CzcCBA efflux system. Finally, we observed an induction of cadA and czcCBA efflux systems upon phagocytosis of P. aeruginosa by macrophages, in which a toxic metal boost is discharged into the phagolysosome to intoxicate microbes. Importantly, we demonstrated that the regulatory link between induction of the CzcCBA system and the repression of the OprD porin responsible for carbapenem antibiotic resistance, is maintained in the macrophage environment.

Directed evolution of a transcription factor PbrR to improve lead selectivity and reduce zinc interference through dual selection

Directed evolution has been proven as a powerful tool for developing proteins and strains with novel or enhanced features. In this study, a dual selection system was designed to tune the binding specificity of a transcription factor to a particular ligand with the ampicillin resistance gene amp (ON selection) as the positive selection marker and the levansucrase gene sacB (OFF selection) as the negative selection marker. It was applied to the lead responsive transcription factor PbrR in a whole-cell lead biosensor previously constructed in our lab (Jia et al. in Fems Microbiol Lett 365:fny157, 2018). After multiple rounds of ON–OFF selection, two mutants with higher specificity for lead were selected. Structural analysis revealed that the mutation C134 located on the metal-binding loop at the C-terminal of PbrR is likely associated with the enhanced binding to both lead and cadmium. The double mutations D64A and L68S close to the metal-binding residue C79 may lead to the reduced binding specificity toward zinc ions. This dual selection system can be applied to engineer the specificity of other transcription factors and provide fine-tuned tools to synthetic biology.

Soil Biodiversity Integrates Solutions for a Sustainable Future

Soils are home to more than 25% of the earth’s total biodiversity and supports life on land and water, nutrient cycling and retention, food production, pollution remediation, and climate regulation. Accumulating evidence demonstrates that multiple sustainability goals can be simultaneously addressed when soil biota are put at the center of land management assessments; this is because the activity and interactions of soil organisms are intimately tied to multiple processes that ecosystems and society rely on. With soil biodiversity at the center of multiple globally relevant sustainability programs, we will be able to more efficiently and holistically achieve the Sustainable Development Goals and Aichi Biodiversity Targets. Here we review scenarios where soil biota can clearly support global sustainability targets, global changes and pressures that threaten soil biodiversity, and actions to conserve soil biodiversity and advance sustainability goals. This synthesis shows how the latest empirical evidence from soil biological research can shape tangible actions around the world for a sustainable future.

Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

Background

Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.

Results

The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424^T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni²⁺ and Zn²⁺ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.

Conclusions

STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine

The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold–copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid – pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.

Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.

Metal nanoparticles fabricated by green chemistry using natural extracts: biosynthesis, mechanisms, and applications

Nanoparticles (NPs) are new inspiring clinical targets that have emerged from persistent efforts with unique properties and diverse applications. However, the main methods currently utilized in their production are not environmentally friendly. With the aim of promoting a green approach for the synthesis of NPs, this review describes eco-friendly methods for the preparation of biogenic NPs and the known mechanisms for their biosynthesis. Natural plant extracts contain many different secondary metabolites and biomolecules, including flavonoids, alkaloids, terpenoids, phenolic compounds and enzymes. Secondary metabolites can enable the reduction of metal ions to NPs in eco-friendly one-step synthetic processes. Moreover, the green synthesis of NPs using plant extracts often obviates the need for stabilizing and capping agents and yields biologically active shape- and size-dependent products. Herein, we review the formation of metallic NPs induced by natural extracts and list the plant extracts used in the synthesis of NPs. In addition, the use of bacterial and fungal extracts in the synthesis of NPs is highlighted, and the parameters that influence the rate of particle production, size, and morphology are discussed. Finally, the importance and uniqueness of NP-based products are illustrated, and their commercial applications in various fields are briefly featured.

The increasing threat of silver-resistance in clinical isolates from wounds and burns

Purpose

The widespread use of silver-containing compounds has led to emergence of silver-resistant bacteria. Few studies are available on the detectability of plasmid-mediated silver-resistance in developing countries. Therefore, we aimed to detect silver-resistance in isolates from wounds and burns, and to genetically characterize plasmid-mediated silver-resistance genes (sil genes).

Methods

One hundred and fifty clinical isolates were obtained from burns and wounds. They were identified using the suitable Analytical Profile Index and MicroScan identification systems. Their antimicrobial susceptibility was tested by the disk diffusion and broth microdilution methods. Their silver nitrate (AgNO₃) minimum inhibitory concentration (MIC) was determined using the broth macrodilution method. The presence of different sil genes on plasmids extracted from silver-resistant isolates and the replicon types of the extracted plasmids were investigated using polymerase chain reaction (PCR). The ability of these plasmids to impart silver-resistance was tested by transformation.

Results

All except two isolates were multidrug-resistant. Nineteen silver-resistant bacterial isolates (12.6%) were detected; with AgNO₃ MIC ≥512 µg/mL. They were identified as Klebsiella pneumoniae (n=7), Staphylococcus aureus (n=4), Escherichia coli (n=2), Enterobacter cloacae (n=2), Pseudomonas aeruginosa (n=2) and Acinetobacter baumannii (n=2). PCR revealed the presence of different sil genes on the extracted plasmids. Plasmid transformation resulted in the transfer of silver-resistance to the resulting transformants. The extracted plasmids had different replicon types.

Conclusion

Plasmid-mediated silver-resistance was detected for the first time, in clinical P. aeruginosa, A. baumannii and S. aureus isolates; in addition to its detection in K. pneumoniae, E. coli and Enterobacter cloacae. Therefore, strict monitoring on the use of silver compounds in medical settings is required; with implementation of an approved standardized method for silver-resistance detection.

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.

Molecular insight into the expression of metal transporter genes in Chryseobacterium sp. PMSZPI isolated from uranium deposit

Metal tolerant bacterium Chryseobacterium sp. PMSZPI previously isolated and characterized from uranium ore deposit was studied for elucidating the role of metal transporter genes belonging to the Cation Diffusion Facilitator (CDF), Root-Nodulation-Division (RND) and PIB-type ATPase family in cadmium and uranium tolerance. The bacterium showed tolerance towards cadmium (MIC~6mM) and uranium (MIC~2mM) and was found to harbor metal transporter genes belonging to CDF, RND and PIB-type ATPase family of proteins. Expression studies by real-time PCR showed an upregulation of czcA(RND), czcD(CDF) and cadA(PIB-type ATPase) genes in presence of cadmium or uranium. Higher expression of czcA and czcD was found when the bacterium was treated with cadmium and uranium respectively. This study provides significant insight into the molecular mechanism that plays a role in cadmium and uranium tolerance in bacteria.

Pseudomonas syringae pv. syringae Associated With Mango Trees, a Particular Pathogen Within the "Hodgepodge" of the Pseudomonas syringae Complex

The Pseudomonas syringae complex comprises different genetic groups that include strains from both agricultural and environmental habitats. This complex group has been used for decades as a "hodgepodge," including many taxonomically related species. More than 60 pathovars of P. syringae have been described based on distinct host ranges and disease symptoms they cause. These pathovars cause disease relying on an array of virulence mechanisms. However, P. syringae pv. syringae (Pss) is the most polyphagous bacterium in the P. syringae complex, based on its wide host range, that primarily affects woody and herbaceous host plants. In early 1990s, bacterial apical necrosis (BAN) of mango trees, a critical disease elicited by Pss in Southern Spain was described for the first time. Pss exhibits important epiphytic traits and virulence factors, which may promote its survival and pathogenicity in mango trees and in other plant hosts. Over more than two decades, Pss strains isolated from mango trees have been comprehensively investigated to elucidate the mechanisms that governs their epiphytic and pathogenic lifestyles. In particular, the vast majority of Pss strains isolated from mango trees produce an antimetabolite toxin, called mangotoxin, whose leading role in virulence has been clearly demonstrated. Moreover, phenotypic, genetic and phylogenetic approaches support that Pss strains producers of BAN symptoms on mango trees all belong to a single phylotype within phylogroup 2, are adapted to the mango host, and produce mangotoxin. Remarkably, a genome sequencing project of the Pss model strain UMAF0158 revealed the presence of other factors that may play major roles in its different lifestyles, such as the presence of two different type III secretion systems, two type VI secretion systems and an operon for cellulose biosynthesis. The role of cellulose in increasing mango leaf colonization and biofilm formation, and impairing virulence of Pss, suggests that cellulose may play a pivotal role with regards to the balance of its different lifestyles. In addition, 62-kb plasmids belonging to the pPT23A-family of plasmids (PFPs) have been strongly associated with Pss strains that inhabit mango trees. Further, complete sequence and comparative genomic analyses revealed major roles of PFPs in detoxification of copper compounds and ultraviolet radiation resistance, both improving the epiphytic lifestyle of Pss on mango surfaces. Hence, in this review we summarize the research that has been conducted on Pss by our research group to elucidate the molecular mechanisms that underpin the epiphytic and pathogenic lifestyle on mango trees. Finally, future directions in this particular plant-pathogen story are discussed.

Comparative genome analysis of completely sequenced Cupriavidus genomes provides insights into the biosynthetic potential and versatile applications of Cupriavidus alkaliphilus ASC-732

The genome analysis of microorganisms provides valuable information to endorse more extensive research on their potential applications. In this paper, the genome of Cupriavidus alkaliphilus ASC-732, isolated from agave rhizosphere in northeastern Mexico, was analyzed and compared with the genomes of other Cupriavidus species to gain better insight into the parts in the genetic makeup responsible for essential metabolic pathways and others of biotechnological importance. Here, the key genes related to glycolysis, pentose phosphate, and the Entner-Doudoroff and tricarboxylic acid cycle pathways were predicted. Comparative genome analysis revealed that the key genes for hydrogenotrophic growth and carbon fixation pathway, i.e., those coding for hydrogenase and enzymes Calvin-Benson-Bassham cycle, are absent in C. alkaliphilus ASC-732. Furthermore, capabilities for producing polyhydroxyalkanoates and extracellular polysaccharide matrix and degrading xenobiotics were found, and the related pathways are explained. Moreover, biofilm formation and the production of exopolysaccharides and polyhydroxyalkanoates were corroborated with crystal violet staining, calcofluor, and Nile red fluorochromes, confirming the presence of the products of the active genes in these pathways and their related metabolic routes, respectively. Additionally, a large group of genes essential for the resistance and detoxification of several heavy metals were also found. Thus, the present study demonstrates that this strain can respond to various environmental signals, such as energy source, nutrient limitations, virulence, and extreme metals concentration, indicating the possibility to foster C. alkaliphilus ASC-732 in diverse biotechnological applications.

Stability of in situ immobilization of trace metals with different amendments revealed by microbial 13C-labelled wheat root decomposition and efflux-mediated metal resistance of soil bacteria

The aim of the present study was to prove the long-term efficiency of the amendments zerovalent iron grit, zeolite, and Divergan® for trace metal remediation in heavily contaminated soils and to attain a recovery of microbial functionality and diversity by remediation. For immobilization of the trace metals the amendments zerovalent iron grit, natural zeolite, and Divergan® were used. Trace metal total and mobile contents were determined and bacterial communities were assessed after a SIP experiment with ¹³C-labelled wheat root by Ion-Torrent Sequencing targeting the bacterial 16S rRNA gene and two trace metal resistant genes for copper and cadmium (copA and czcA gene). The results show that the remediation effect of the three amendments is still stable after five years. The mobile trace metal contents were significantly (≤0.001) reduced in all treatments, except the Cu content in the zeolite treatment. A higher diversity in active metabolizing and growing soil bacteria was observed in remediated soils as compared to the non-remediated control, especially for the Divergan® treatment. The bacterial genera Kribbella, Glycomyces, Inquilinus, Nocardioides, and Lysobacter are the most significantly enriched genera in the ¹³C fractions of the treated samples. The occurrence of bacterial families, which could be identified carrying efflux-mediated metal resistance genes for Cd/Zn and Cu, were reduced in the remediated soils as compared to the non-remediated control. The most abundant bacterial family for the copA and the czcA gene is Xanthomonadaceae. The pH-value and the trace metal concentration could be identified as key drivers of bacterial community composition, and functions in trace metal contaminated soils and remediated soils.

Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation

Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.

Genomic and Transcriptomic Changes that Mediate Increased Platinum Resistance in Cupriavidus metallidurans

The extensive anthropogenic use of platinum, a rare element found in low natural abundance in the Earth's continental crust and one of the critical raw materials in the EU innovation partnership framework, has resulted in increased concentrations in surface environments. To minimize its spread and increase its recovery from the environment, biological recovery via different microbial systems is explored. In contrast, studies focusing on the effects of prolonged exposure to Pt are limited. In this study, we used the metal-resistant Cupriavidus metallidurans NA4 strain to explore the adaptation of environmental bacteria to platinum exposure. We used a combined Nanopore⁻Illumina sequencing approach to fully resolve all six replicons of the C. metallidurans NA4 genome, and compared them with the C. metallidurans CH34 genome, revealing an important role in metal resistance for its chromid rather than its megaplasmids. In addition, we identified the genomic and transcriptomic changes in a laboratory-evolved strain, displaying resistance to 160 µM Pt4+. The latter carried 20 mutations, including a large 69.9 kb deletion in its plasmid pNA4_D (89.6 kb in size), and 226 differentially-expressed genes compared to its parental strain. Many membrane-related processes were affected, including up-regulation of cytochrome c and a lytic transglycosylase, down-regulation of flagellar and pili-related genes, and loss of the pNA4_D conjugative machinery, pointing towards a significant role in the adaptation to platinum.

Spontaneous mutation in the AgrRS two-component regulatory system ofCupriavidus metalliduransresults in enhanced silver resistance

Cupriavidus metalliduransis able to adapt to toxic silver concentrations and previously uncharacterized periplasmic proteins played a crucial role in this adaptation process.

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine

Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu^(II), 21 mM Zn^(II), 1.2 mM Cd^(II), and 10.0 mM As^(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P_IB-1-ATPase, 5 putative P_IB-3-ATPase, 4 putative Zn^(II)/Cd^(II) P_IB-4 type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance

For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.