A case of convergent evolution: Several viral and bacterial pathogens hijack RSK kinases through a common linear motif.

Microbes have been coevolving with their host for millions of years, exploiting host resources to their own benefit. We show that viral and bacterial pathogens convergently evolved to hijack cellular mitogen-activated protein kinase (MAPK) p90-ribosomal S6-kinases (RSKs). Theiler's virus leader (L) protein binds RSKs and prevents their dephosphorylation, thus maintaining the kinases active. Recruitment of RSKs enables L-protein-mediated inhibition of eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2 or PKR) and stress granule formation. Strikingly, ORF45 protein of Kaposi's sarcoma-associated herpesvirus (KSHV) and YopM protein of Yersinia use the same peptide motif as L to recruit and activate RSKs. All three proteins interact with a conserved surface-located loop of RSKs, likely acting as an allosteric regulation site. Some unrelated viruses and bacteria thus evolved to harness RSKs in a common fashion, yet to target distinct aspects of innate immunity. As documented for Varicella zoster virus ORF11, additional pathogens likely evolved to hijack RSKs, using a similar short linear motif.

SARS-CoV-2 nucleocapsid antigen in plasma of children hospitalized for COVID-19 or with incidental detection of SARS-CoV-2 infection.

In hospitalized children, SARS-CoV-2 infection can present as either a primary reason for admission (patients admitted for COVID-19) or an incidental finding during follow-up (patients admitted with COVID-19). We conducted a nested case-control study within a cohort of pediatric patients with confirmed SARS-CoV-2 infection, to investigate the concentration of plasma nucleocapsid antigen (N-Ag) in children admitted for COVID-19 or with COVID-19. While reverse transcriptase polymerase chain reaction Ct values in nasopharyngeal swab were similar between the two groups, children admitted for COVID-19 had a higher rate of detectable N-Ag (12/18 (60.7%) versus 6/18 (33.3%), p = 0.0455) and a higher concentration of N-Ag (medians: 19.51 g/mL vs. 1.08 pg/mL, p = 0.0105). In children hospitalized for COVID-19, the youngest had higher concentration of N-Ag (r = -0.74, p = 0.0004). We also observed a lower prevalence of detectable spike antibodies in children hospitalized for COVID-19 compared to those hospitalized for other medical reasons (3/15 [20%] vs. 13/16 [81.25%], respectively, p = < 0.0011), but similar rates of IgG nucleocapsid antibodies (5/14 [35.7%] vs. 6/17 [35.3%], respectively, p = 0.99). Our findings indicate that N-Ag is associated with COVID-19-related hospitalizations in pediatric patients, and less frequently detected in children tested positive for SARS-CoV-2 but hospitalized for another medical reason. Further studies are needed to confirm the value of N-Ag in identifying COVID-19 disease infections in which SARS-CoV-2 is the main pathogen responsible for symptoms.

The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils.

Mercury (Hg) pollution is a global issue due to the high toxicity and wide dispersion of Hg around the world. Whether due to anthropogenic activities or natural processes, Hg emissions are steadily increasing, with very high levels in some regions, directly threatening human and ecosystem health. However, bacteria and fungi have evolved and adapted in response to Hg-induced stress and have developed tolerance mechanisms, notably based on the mer operon system that is involved in Hg uptake and biovolatilization via Hg reduction reactions. Other processes, such as bioaccumulation or extracellular sequestration, are involved in Hg resistance, and the study of contaminated soils has allowed the isolation of a number of microorganisms capable of these mechanisms, with strong potential for the implementation of bioremediation approaches. In addition to playing an important role in determining the fate of Hg in the biogeochemical cycle, these microorganisms can indeed be applied to reduce Hg concentrations or at least stabilize Hg for the remediation of polluted soils. Moreover, thanks to the development of biotechnological tools, bioremediation based on Hg-tolerant microorganisms can be optimized. Finally, these microorganisms are relevant candidates for biomonitoring, for example, through the engineering of biosensors, because the detection of Hg is a major issue in preserving the health of living beings.

Vectorial Release of Hepatitis E Virus in Polarized Human Hepatocytes.

Hepatitis E virus (HEV) is a common cause of acute viral hepatitis worldwide. Most HEV infections are asymptomatic, but immunocompromised patients infected with HEV genotype 3 (HEV3), HEV4, or HEV7 may develop chronic infections. The HEV particles in stools are naked (nHEV), while those in the serum and culture supernatants (eHEV) are associated with lipids. Hepatocytes are polarized epithelial cells that have basolateral (oriented toward the blood) and apical (oriented toward the bile) exosomal pathways. We isolated a subclone, F2, from the human hepatocarcinoma cell line HepG2/C3A that grew as a polarized monolayer culture and had better HEV production than HepG2/C3A cells. F2 cells cultured on semipermeable collagen inserts and infected basolaterally with nHEV3 released 94.6% of virus particles apically, those infected with eHEV3 released 96.8% apically, and eHEV1-infected cells released 99.3% apically. Transcytosis was not involved. Density gradient centrifugation and NP-40 treatment showed that HEV particles released both apically and basolaterally were lipid associated. The apically released HEV3 and HEV1 particles were six and nine times more infectious than those released basolaterally, respectively. Confocal microscopy indicated that the open reading frame 2 (ORF2) capsid protein colocalized apically with ORF3 virus protein, the apical marker DPP4, and the recycling endosome GTPase Rab27a. The amounts of soluble glycosylated ORF2 secreted apically and basolaterally were similar. These polarized-hepatocyte data suggest that infectious HEV particles are mainly released into bile, while the small fraction released into blood could spread HEV throughout the host.IMPORTANCE Hepatitis E virus (HEV) in stools is naked, while that in culture supernatants and patients' blood is lipid associated. Its life cycle in hepatocytes, polarized cells with a basolateral side communicating with blood and an apical side connected with bile, is incompletely understood. We have developed a polarized hepatocyte model and used the cells to analyze the supernatants bathing the apical and basolateral sides and HEV subcellular distribution. HEV particles from both sides were lipid associated, and most infectious HEV particles left the cell via its apical side. Similar amounts of the open reading frame 2 (ORF2) soluble capsid protein were secreted from both sides of the hepatocytes. This model mimicking physiological conditions should help clarify the HEV cell cycle in polarized hepatocytes.

Impact of ageing and soil contaminants on telomere length in the land snail.

Telomeres (TLs) are non-coding DNA sequences that are usually shortened with ageing and/or chemical exposure. Bioindicators such as the land snail can be used to assess the environmental risk of contaminated soils. As for most invertebrates, the evolution of TLs with ageing or exposure to contaminants is unknown in this mollusc. The aims of this study were to explore the relationships between ageing, contaminant exposure, sublethal effects and TL length in the terrestrial gastropod Cantareus aspersus. TL length was investigated in haemocytes from five age classes of C. aspersus. The impact of contaminants on sub-adult snails exposed to Cd, Hg or a mixture of polycyclic aromatic hydrocarbons (PAHs) in soils for one or two months was studied. Bioaccumulation, growth, sexual maturity and TLs were measured. TL attrition was significant for the juvenile and sub-adult stages, but not later. Exposure to Cd increased the mortality (around 30%). Exposure to polluted soils inhibited growth (19-40%) and sexual maturity (6-100%). Although the health of the snails exposed to Cd, Hg and PAHs was altered, TL length in haemocytes was not disturbed, suggesting a high capacity of this snail species to maintain its TLs in haemocytes under chemical stress. These results first address TL length in snails and reveal that the relationship commonly proposed for vertebrates between TL shortening and ageing or exposure to contaminants cannot be generalized.

[Hepatitis E virus: from the infected organism to the cellular response]. / Virus de l'hépatite E : de l'organisme infecté à la réponse cellulaire.

Hepatitis E virus (HEV) presents a worldwide distribution. In developing countries, hepatitis E, related to HEV1 and HEV2, is a waterborne disease. In developed countries, hepatitis E is a zoonotic disease due to HEV3 and HEV4. It is mainly transmitted through meat consumption from animal reservoirs such as pig, boar, deer and rabbit. New clinical forms include neurological manifestations that are now clearly associated with HEV3 infection. Recent studies showed that ORF1 polyprotein was able to disrupt the innate immune response. It was also shown that ORF2 protein exists at least in two forms: a free, glycosylated form and a non-glycosylated form, which assembles to form the capsid. Lastly, it was shown that ORF3 protein, involved in the virus egress, acts as a viroporin. New culture systems and animal models have been developed recently, and will be very helpful to complete our understanding of HEV life cycle and pathogenesis.

First amplification of Eimeria hessei DNA from the lesser horseshoe bat (Rhinolophus hipposideros) and its phylogenetic relationships with Eimeria species from other bats and rodents.

Although coccidian parasites of the genus Eimeria are among the best-documented parasites in bats, few Eimeria species found in bats have been characterised using molecular tools, and none of the characterised species are found in European countries. Phylogenetic relationships of Eimeria species that parasitise bats and rodents can be related to the morphology of oocysts, independently from host range, suggesting that these species are derived from common ancestors. In the present study, we isolated a partial sequence of the Eimeria hessei 18S rRNA gene from the lesser horseshoe bat (Rhinolophus hipposideros), a European bat species. Droppings from lesser horseshoe bats were collected from 11 maternity roosts located in France that were positive for the presence of the parasite. Through morphological characterisation, the oocysts detected in the lesser horseshoe bat droppings were confirmed to be E. hessei. The unique E. hessei sequence obtained through molecular analysis belonged to a clade that includes both rodent and bat Eimeria species. However, the E. hessei oocysts isolated from the bat droppings did not show morphological similarities to rodent Eimeria species.

An assessment of the embryotoxicity of cadmium in the terrestrial mollusk Cantareus aspersus: from bioaccumulation to impacts at different levels of biological organization.

This study aims to determine various parameters that allow the evaluation of the toxicity of chemicals to embryos of the ubiquitous land snail Cantareus aspersus. For this purpose, we investigated morphological and physiological endpoints in control embryos and in embryos exposed to a solution of 6mg Cd/L (CdCl2) in a liquid phase bioassay: size at days 3, 6 and 10, heart rate at 7 days, delay in hatching, states of development of non-hatched eggs after 17 days and the fresh mass of newly hatched embryos. The kinetics of Cd accumulation in eggs and DNA fragmentation were also measured. The first detectable sign of adverse effects appeared after 7 days of development, when the heart rate decreased in Cd-exposed embryos compared with the control. After 10 days of exposure, Cd-exposed hatchlings exhibited a lower fresh mass than control individuals. The majority (75 percent) of non-hatched embryos at 17 days was dead and presented signs of disaggregation or malformations. The hatching of Cd-exposed eggs was delayed 4 days, and DNA fragmentation was later detected after 20 days of Cd exposure. The measurement of Cd in the eggs showed that concentrations are relatively stable during the exposure period from 3 days (20-27µg Cd/g DW) to the end of exposure. The present study completes the range of endpoints that can be used to study the effects of contaminants and provides new parameters that are readily measured throughout the embryonic development of a terrestrial mollusk.

First evidence of fish genotoxicity induced by heavy metals from landfill leachates: the advantage of using the RAPD-PCR technique.

Municipal leachates are loaded with heavy metals that can contaminate surface water before discharge into a receiving body of water. The aim of this study is to evaluate the genotoxic effects of heavy metals generated by domestic waste on the common roach Rutilus rutilus in the last of the four interconnected ponds at the Etueffont landfill. We used random amplified polymorphic DNA (RAPD) since it has been shown to be a powerful means of detecting a broad range of DNA damage due to environmental contaminants. Our results show the ability of RAPD analysis to detect significant genetic alterations in roach DNA, after contamination with a set of metals contained in the landfill leachates in comparison to a roach from a non-polluted reference pond. Analysis of electrophoresis profiles indicates apparent changes such as the appearance of new bands or disappearance of bands as compared to the control. In fact, mixed smearing and laddering of DNA fragments in muscle samples support the genotoxic effects of metal deposits in the roach. This study is the first evidence found via the RAPD-PCR technique in the detection of pollutant impacts on fish exposed to landfill leachates.

Coupling of random amplified polymorphic DNA profiles analysis and high resolution capillary electrophoresis system for the assessment of chemical genotoxicity.

Cadmium (Cd) can be toxic to terrestrial snails, but few data are available about its genotoxic effects on early life stages (ELS). The aim of this study was to investigate the genotoxic potential of Cd in embryos of Helix aspersa using a new approach that couples Random Amplified Polymorphic DNA (RAPD) and a high-resolution capillary electrophoresis system (HRS). Clutches of H. aspersa were exposed to Cd solutions (2, 4, and 6 mg/L) from the beginning of their embryonic development. In addition to a dose-dependent effect of Cd on hatching rate, DNA fragmentation was observed in embryos that were exposed to 6 mg Cd/L. The analysis of RAPD products with HRS showed differences between the profiles of exposed and nonexposed embryos, starting at 2 mg Cd/L. In comparison to the profiles of the control samples, all profiles from the exposed snails exhibited an additional 270 bp DNA fragment and lacked a 450 bp DNA fragment. These profile modifications are related to the genotoxic effect of Cd on the ELS of H. aspersa . Our study demonstrates the efficacy of coupling RAPD and HRS for a rapid and efficient screening of the effects of chemicals on DNA.

Ecogenotoxicity assessment with land snails: A mini-review.

In the context of the increasing environmental and sanitary crisis, it is accepted that soil pollution can cause health alterations and disturb natural population dynamics. Consequently, the assessment of the genotoxic potential of compounds found in contaminated soils is important. Indeed, the alteration of genomic integrity may increase the risk of cancer development and may impair reproduction and long-term population dynamics. Among the methodologies to assess terrestrial genotoxic potential, there has been growing interest during the last decade in monitoring alterations of the genome in bioindicators of soil quality. As some land snail species are recognized bioindicators of soil quality, especially to assess the environmental and toxicological bioavailability of compounds, this review focuses on current knowledge regarding the genotoxicology of land snails. Classical biomarkers to assess genotoxic effects have been used (e.g., DNA breakage, micronuclei, random amplification polymorphic DNA) at various stages of the life cycle, including embryos. The studies were performed in vitro, in vivo, in situ and ex situ and covered a diverse set of contaminants (nanoparticles, metal(loid)s, pesticides, polycyclic aromatic hydrocarbons) and snail species (Cantareus aspersus, Eobania vermiculata, Theba pisana, Helix lucorum). Based on recent studies reviewed here, the use of land snails to map soil genotoxic potential is promising due to their ability to reveal pollution and subsequent environmental risks. Moreover, the position of snails in the trophic chain and the existing bridges between contaminant bioavailability to snails and bioaccessibility to humans reinforce the value of land snail-based ecotoxicological assessment.

From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium.

Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.

Vectorial Release of Human RNA Viruses from Epithelial Cells.

Epithelial cells are apico-basolateral polarized cells that line all tubular organs and are often targets for infectious agents. This review focuses on the release of human RNA virus particles from both sides of polarized human cells grown on transwells. Most viruses that infect the mucosa leave their host cells mainly via the apical side while basolateral release is linked to virus propagation within the host. Viruses do this by hijacking the cellular factors involved in polarization and trafficking. Thus, understanding epithelial polarization is essential for a clear understanding of virus pathophysiology.

Contrasting growth and adaptive responses of two oak species to flooding stress: role of non-symbiotic haemoglobin.

Soil flooding is an environmental constraint that is increasingly important for forest ecosystems, affecting tree growth and regeneration. As a result, selection pressure will alter forest diversity and distribution by favouring tree species tolerant of soil oxygen deprivation. Sessile and pedunculate oaks are the most abundant oak species and they exhibit a strong differential tolerance to waterlogging. In order to gain some understanding of the mechanisms of tolerance of both species to hypoxia, we undertook the characterization of the physiological, morphological, cellular and molecular responses of both species to flooding stress. Our results indicate that pedunculate oak, the more tolerant species, succeeded in maintaining its growth, water status and photosynthetic activity at a higher level than sessile oak. Furthermore, pedunculate oak developed aerenchyma in its root cortex as well as adventitious roots. The later exhibited a strong accumulation of class1 non-symbiotic haemoglobin localized by in situ hybridization in the protoderm and in some cortical cells. In conclusion, the higher tolerance of pedunculate oak to flooding was associated with an enhanced capacity to maintain photosynthesis and water homeostasis, coupled with the development of adaptive features (aerenchyma, adventitious roots) and with a higher expression of non-symbiotic haemoglobin in the roots.

From environmental bioavailability of metal(loid)s to their ecogenotoxicological effects in land snails.

To date, no study has linked the environmental and the ecogenotoxicological bioavailability of contaminants to land snails. Yet, understanding the specific ecotoxicological mechanisms from bioaccumulation to genotoxicity is necessary e.g., to build an adverse outcome pathway relevant to risk assessment. Consequently, the aim of our study is to look for relationships between accumulated concentrations of As, Cd and Hg in sub-adult snails and ecotoxicological effects at the individual (survival and growth) and molecular (genomic stability) levels. This study combines random amplified polymorphic DNA (RAPD) coupled with high-resolution capillary electrophoresis system (HRS) and micronucleus (MN) assay on haemocytes to consider various types of cytogenomic damage, such as chromosomal aberrations, breakages, adducts and mutations. The results showed alteration of the individual endpoints at higher accumulation quotients (AQs) that reflect the excess of transfers to snails, especially with decreased survival for As. In addition, genotoxic effects were observed with an increased occurrence of MN in haemocytes for the three meta(loid)s considered (R2 from 0.57 to 0.61 as a function of the meta(loid)s). No concentration-dependent decrease in genome stability was highlighted by RAPD-HRS in snails exposed to As and Cd but not Hg. Our results demonstrate the complementarity of the RAPD-HRS and the MN assay for understanding the different genotoxic mechanisms of the three metal(loid)s studied in land snails. They show a way to better assess environmental risks of contaminated soils by associating ecotoxicity, genotoxicity and bioaccumulation assays (ISO 24032), i.e., ecogenotoxicological bioavailability. Convergences highlighted here between the bioaccumulation of metal(loid)s in viscera and genotoxic effects in haemocytes constitute a way to better assess the bioavailability of contaminants in soils to the land snail and the subsequent environmental risk.

Optimized Hepatitis E Virus (HEV) Culture and its Application to Measurements of HEV Infectivity.

Hepatitis E virus (HEV) is a major concern in public health worldwide. Infections with HEV genotypes 3, 4, or 7 can lead to chronic hepatitis while genotype 1 infections can trigger severe hepatitis in pregnant women. Infections with all genotypes can worsen chronic liver diseases. As virions are lipid-associated in blood and naked in feces, efficient methods of propagating HEV clinical strains in vitro and evaluating the infectivity of both HEV forms are needed. We evaluated the spread of clinical strains of HEV genotypes 1 (HEV1) and 3 (HEV3) by quantifying viral RNA in culture supernatants and cell lysates. Infectivity was determined by endpoint dilution and calculation of the tissue culture infectious dose 50 (TCID50). An enhanced HEV production could be obtained varying the composition of the medium, including fetal bovine serum (FBS) and dimethylsulfoxide (DMSO) content. This increased TCID50 from 10 to 100-fold and allowed us to quantify HEV1 infectivity. These optimized methods for propagating and measuring HEV infectivity could be applied to health safety processes and will be useful for testing new antiviral drugs.

Hepatitis E virus genotype 3 and capsid protein in the blood and urine of immunocompromised patients.

OBJECTIVES: Hepatitis E virus genotype 3 (HEV3) is responsible for acute and chronic liver disease in solid organ transplant (SOT) recipients. HEV was recently found in the urine of some acutely and chronically genotype 4-infected patients. METHODS: We examined the urinary excretion of HEV3 by 24 consecutive SOT recipients at the acute phase of HEV hepatitis and characterized the excreted virus. RESULTS: Urinary HEV RNA was detected in 12 (50%) of the 24 transplanted patients diagnosed with HEV hepatitis. Urinary HEV antigen (Ag) was detected in all but one of the patients (96%). The density of RNA-containing HEV particles in urine was low (1.11-1.12 g/cm3), corresponding to lipid-associated virions. The urinary HEV RNA/Ag detected was not associated with impaired kidney function or de novo proteinuria. Finally, there was more HEV Ag in the serum at the acute phase of HEV infection in SOT recipients whose infection became chronic. CONCLUSIONS: HEV3 excreted via the urine of SOT recipients at the acute phase of HEV hepatitis has a lipid envelope. Renal function was not impaired. While urinary HEV Ag was a sensitive indicator of HEV infection, only acute phase serum HEV Ag indicated the development of a chronic infection.

Hepatitis E virus infections in Europe.

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. The systematic use of improved tools for diagnosing and genotyping has completely changed our understanding of the epidemiology and clinical consequences of HEV infection. Most cases of HEV in Europe arise from infected animals such as pigs, wild boar, deer and rabbits. Zoonotic HEV genotypes (HEV genotypes 3-8) are mainly food-borne or transmitted by direct contact, but recent data suggest that infection can also be water-borne or even iatrogenic throught contamined blood products. HEV-3 is the most prevalent genotype in Europe but the geographic distributions of the 3 major clades and subgenotypes (HEV-3abjkchi, HEV-3efg, and HEV-3ra) differ. Most HEV-3 infections are asymptomatic but they can result in severe acute hepatitis in patients with chronic liver disease, chronic hepatitis in immunocompromised patients, and to extra-hepatic manifestations. Despite more frequent reports of symptomatic hepatitis E cases across Europe, systems for monitoring HEV infections vary greatly. Severe HEV-associated illnesses, hospitalizations and deaths are probably underestimated. The seroprevalence and incidence of locally acquired hepatitis E varies between and within European countries and over time. The precise origin of these variations is uncertain but may be linked to environmental factors or the degree to which HEV contaminates the human food chain. Collaborative initiatives such as the establishment of the One Health platform for HEV sequences (HEVnet database) will be very useful for a better understanding of the epidemiology of HEV in Europe and the development of effective prevention strategies.

[Reactive oxygen species, stress and cell death in plants]. / Formes réactives de l'oxygène, stress et mort cellulaire chez les plantes.

Plants are constantly exposed to changes in environmental conditions. During periods of stress, the cellular redox homeostasis is altered as a result of reactive oxygen species accumulation. The change in redox is responsible for the symptoms commonly observed during periods of stress and reflects the phytotoxic nature of oxygen radical accumulation. However, oxygen radicals have recently been identified as key actors in the response to stress and their role as secondary messengers is now clearly established. The identification of their role in gene regulation has allowed one to identify them as key regulators in the induction and execution of programmed cell death typically observed during developmental processes as well as during stress responses. This review presents recent advances in the characterisation of the role of reactive oxygen species in plants.

Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill.

The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.