ytiB and ythA Genes Reduce the Uranium Removal Capacity of Bacillus atrophaeus

The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history

Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.

Independent and synergistic bio-reductions of uranium (VI) driven by zerovalent iron in aquifer

Zerovalent iron [Fe(0)] can donate electron for bioprocess, but microbial uranium (VI) [U(VI)] reduction driven by Fe(0) is still poorly understood. In this study, Fe(0) supported U(VI) bio-reduction was steadily achieved in the 160-d continuous-flow biological column. The maximum removal efficiency and capacity of U(VI) were 100% and 46.4 ± 0.52 g/(m³·d) respectively, and the longevity of Fe(0) increased by 3.09 times. U(VI) was reduced to solid UO₂, while Fe(0) was finally oxidized to Fe(III). Autotrophic Thiobacillus achieved U(VI) reduction coupled to Fe(0) oxidation, verified by pure culture. H₂ produced from Fe(0) corrosion was consumed by autotrophic Clostridium for U(VI) reduction. The detected residual organic intermediates were biosynthesized with energy released from Fe(0) oxidation and utilized by heterotrophic Desulfomicrobium, Bacillus and Pseudomonas to reduce U(VI). Metagenomic analysis found the upregulated genes for U(VI) reduction (e.g., dsrA and dsrB) and Fe(II) oxidation (e.g., CYC1 and mtrA). These functional genes were also transcriptionally expressed. Cytochrome c and glutathione responsible for electron transfer also contributed to U(VI) reduction. This study reveals the independent and synergistic pathways for Fe(0)-dependent U(VI) bio-reduction, providing promising remediation strategy for U(VI)-polluted aquifers.

Biosorption and biomineralization of U(VI) by Kocuria rosea: Involvement of phosphorus and formation of U-P minerals

The biosorption and biomineralization behavior of U(VI) by Kocuria rosea with uranium resistance higher than other general microorganisms was investigated in this study. The results showed the obvious effects of initial U(VI) concentration, biomass, time, and especially pH, and presented that U(VI) was immobilized to K. rosea by physical and chemical action. The characterization results for the precipitation proved that U-P minerals with U(VI) (H₃OUO₂PO₄·3H₂O, H₂(UO₂)₂(PO₄)₂·8H₂O) or U(IV) (CaU(PO₄)₂) were dominant, and the crystallization level increased with time. In the process, the phosphorous containing groups, amino, hydroxyl and carboxyl groups played important roles in adsorption of U(VI), and the phosphate groups were crucial in immobilization of uranium, showing the importance of groups containing phosphorus in both biosorption and biomineralization processes. Our findings focus on the biosorption and biomineralization mechanism of U(VI) by K. rosea, emphasize the synergy of physical adsorption and chemical immobilization in the process and formation of U(VI)-P and U(IV)-P minerals, and highlight the significance of phosphorus involvement in the reaction.

Uranium (U) source, speciation, uptake, toxicity and bioremediation strategies in soil-plant system: A review

Uranium(U), a highly toxic radionuclide, is becoming a great threat to soil health development, as returning nuclear waste containing U into the soil systems is increased. Numerous studies have focused on: i) tracing the source in U contaminated soils; ii) exploring U geochemistry; and iii) assessing U phyto-uptake and its toxicity to plants. Yet, there are few literature reviews that systematically summarized the U in soil-plant system in past decade. Thus, we present its source, geochemical behavior, uptake, toxicity, detoxification, and bioremediation strategies based on available data, especially published from 2018 to 2021. In this review, we examine processes that can lead to the soil U contamination, indicating that mining activities are currently the main sources. We discuss the relationship between U bioavailability in the soil-plant system and soil conditions including redox potential, soil pH, organic matter, and microorganisms. We then review the soil-plant transfer of U, finding that U mainly accumulates in roots with a quite limited translocation. However, plants such as willow, water lily, and sesban are reported to translocate high U levels from roots to aerial parts. Indeed, U does not possess any identified biological role, but provokes numerous deleterious effects such as reducing seed germination, inhibiting plant growth, depressing photosynthesis, interfering with nutrient uptake, as well as oxidative damage and genotoxicity. Yet, plants tolerate U toxicity via various defense strategies including antioxidant enzymes, compartmentalization, and phytochelatin. Moreover, we review two biological remediation strategies for U-contaminated soil: (i) phytoremediation and (ii) microbial remediation. They are quite low-cost and eco-friendly compared with traditional physical or chemical remediation technologies. Finally, we conclude some promising research challenges regarding U biogeochemical behavior in soil-plant systems. This review, thus, further indicates that the combined application of U low accumulators and microbial inoculants may be an effective strategy for the bioremediation of U-contaminated soils.

Multisystem combined uranium resistance mechanisms and bioremediation potential of Stenotrophomonas bentonitica BII-R7: Transcriptomics and microscopic study

The potential use of microorganisms in the bioremediation of U pollution has been extensively described. However, a lack of knowledge on molecular resistance mechanisms has become a challenge for the use of these technologies. We reported on the transcriptomic and microscopic response of Stenotrophomonas bentonitica BII-R7 exposed to 100 and 250 μM of U. Results showed that exposure to 100 μM displayed up-regulation of 185 and 148 genes during the lag and exponential phases, respectively, whereas 143 and 194 were down-regulated, out of 3786 genes (>1.5-fold change). Exposure to 250 μM of U showed up-regulation of 68 genes and down-regulation of 290 during the lag phase. Genes involved in cell wall and membrane protein synthesis, efflux systems and phosphatases were up-regulated under all conditions tested. Microscopic observations evidenced the formation of U-phosphate minerals at membrane and extracellular levels. Thus, a biphasic process is likely to occur: the increased cell wall would promote the biosorption of U to the cell surface and its precipitation as U-phosphate minerals enhanced by phosphatases. Transport systems would prevent U accumulation in the cytoplasm. These findings contribute to an understanding of how microbes cope with U toxicity, thus allowing for the development of efficient bioremediation strategies.