Multiple Transcriptional Mechanisms Collectively Mediate Copper Resistance in Cupriavidus gilardii CR3

Genomic and transcriptomic analyses reveal insights into cadmium resistance mechanisms of Cupriavidus nantongensis strain E324

The cadmium-resistant Cupriavidus sp. strain E324 has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the strain E324 was most closely related to C. nantongensis X1T, indicating that the strain E324 should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. nantongensis strain E324, the transcriptional response of this strain to acute Cd exposure was assessed using RNA-seq-based transcriptome analysis, followed by validation through qRT-PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure. Among these, only the Zn pretreatment resulting in high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis strain E324 via the enhancement of metal-chelating and antioxidant capacities of the cells.

The quorum sensing SinI/SinR-TraI/TraR systems promote Pb stabilization by Ensifer adhaerens S24 in the Pb-polluted aquatic environment

In this study, the Pb-resistant Ensifer adhaerens strain S24, which contains quorum sensing (QS) systems responsible for N-acyl homoserine lactone (AHL) production, was investigated for QS system-mediated Pb stabilization and the underlying mechanisms. Whole-genome sequence analysis revealed the QS SinI/R and TraI/R systems in strain S24. Subsequently, strains S24 and the S24∆sinI/R, S24∆traI/R, S24∆traI/R/sinR, and S24∆sinI/R-traI/R/sinR mutants were constructed and compared for QS SinI/SinR-TraI/TraR system-mediated Pb stabilization in the solution and the mechanisms involved. After 5 days of incubation, strain S24 significantly decreased the Pb concentration in the Pb-contaminated solution compared with the mutants. The S24∆sinI/R-traI/R/sinR mutant exhibited reduced Pb stabilization and AHL activity than the other mutants. The S24∆sinI/R-traI/R/sinR mutant had significantly greater Pb concentrations in the solution and lower cell surface-adsorbed and extracellular precipitated Pb (PbS) contents as well as lower expression of H2S-producing genes of metC and sseA than did strain S24. Furthermore, the S24∆sinI/R-traI/R/sinR mutant displayed reduced interactions between the hydroxyl, amino, carboxyl, and ether groups and Pb, compared with strain S24. These findings implied the vital role of the SinI/SinR-TraI/TraR systems in strain S24 for Pb stabilization through enhanced cell surface adsorption and extracellular precipitation in Pb-polluted aquatic environments.

Influence of Copper on Oleidesulfovibrio alaskensis G20 Biofilm Formation

Copper is known to have toxic effects on bacterial growth. This study aimed to determine the influence of copper ions on Oleidesulfovibrio alaskensis G20 biofilm formation in a lactate-C medium supplemented with variable copper ion concentrations. OA G20, when grown in media supplemented with high copper ion concentrations of 5, 15, and 30 µM, exhibited inhibited growth in its planktonic state. Conversely, under similar copper concentrations, OA G20 demonstrated enhanced biofilm formation on glass coupons. Microscopic studies revealed that biofilms exposed to copper stress demonstrated a change in cellular morphology and more accumulation of carbohydrates and proteins than controls. Consistent with these findings, sulfur (dsrA, dsrB, sat, aprA) and electron transport (NiFeSe, NiFe, ldh, cyt3) genes, polysaccharide synthesis (poI), and genes involved in stress response (sodB) were significantly upregulated in copper-induced biofilms, while genes (ftsZ, ftsA, ftsQ) related to cellular division were negatively regulated compared to controls. These results indicate that the presence of copper ions triggers alterations in cellular morphology and gene expression levels in OA G20, impacting cell attachment and EPS production. This adaptation, characterized by increased biofilm formation, represents a crucial strategy employed by OA G20 to resist metal ion stress.

Effects of Cd(II) on nitrogen removal by a heterotrophic nitrification aerobic denitrification bacterium Pseudomonas sp. XF-4

Simultaneous heterotrophic nitrification and aerobic denitrification (SND) is gaining tremendous attention due to its high efficiency and low cost in water treatment. However, SND on an industrial scale is still immature since effects of coexisting pollutants, for example, heavy metals, on nitrogen removal remains largely unresolved. In this study, a HNAD bacterium (Pseudomonas sp. XF-4) was isolated. It could almost completely remove ammonium and nitrate at pH 5-9 and temperature 20 ℃-35 ℃ within 10 h, and also showed excellently simultaneous nitrification and denitrification efficiency under the coexistence of any two of inorganic nitrogen sources with no intermediate accumulation. XF-4 could rapidly grow again after ammonium vanish when nitrite or nitrate existed. There was no significant effects on nitrification and denitrification when Cd(II) was lower than 10 mg/L, and 95 % of Cd(II) was removed by XF-4. However, electron carrier and electron transport system activity was inhibited, especially at high concentration of Cd(II). Overall, this study reported a novel strain capable of simultaneous nitrification and denitrification coupled with Cd(II) removal efficiently. The results provided new insights into treatment of groundwater or wastewater contaminated by heavy metals and nitrogen.

Elimination of copper obstacle factor in anaerobic digestion effluent for value-added utilization: Performance and resistance mechanisms of indigenous bacterial consortium

The presence of excessive residual Cu(II), a high-risk heavy metal with potential toxicity and biomagnification property, substantially impede the value-added utilization of anaerobic digestion effluent (ADE). This study adapted indigenous bacterial consortium (IBCs) to eliminate Cu(II) from ADE, and their performances and resistance mechanisms against Cu(II) were analyzed. Results demonstrated that when the Cu(II) exposure concentration exceeded 7.5 mg/L, the biomass of IBCs decreased significantly, cells produced a substantial amount of ROS and EPS, at which time the intracellular Cu(II) content gradually decreased, while Cu(II) accumulation within the EPS substantially increased. The combined features of a high PN/PS ratio, a reversed Zeta potential gradient, and abundant functional groups within EPS collectively render EPS a primary diffusion barrier against Cu(II) toxicity. Mutual physiological and metagenomics analyses reveal that EPS synthesis and secretion, efflux, DNA repair along with coordination between each other were the primary resistance mechanisms of IBCs against Cu(II) toxicity. Furthermore, IBCs exhibited enhanced resistance by enriching bacteria carrying relevant resistance genes. Continuous pretreatment of actual ADE with IBCs at a 10-day hydraulic retention time (HRT) efficiently eliminated Cu(II) concentration from 5.01 mg/L to ∼0.68 mg/L by day 2. This elimination remained stable for the following 8 days of operation, further validated their good Cu(II) elimination stability. Notably, supplementing IBCs with 200 mg/L polymerized ferrous sulfate significantly enhanced their settling performance. By elucidating the intricate interplay of Cu(II) toxicity and IBC resistance mechanisms, this study provides a theoretical foundation for eliminating heavy metal barriers in ADE treatment.

Genomic Sequencing of Clinical Cupriavidus gilardii Isolates Revealed Their Diverse Antimicrobial Resistance Mechanisms

Purpose

Cupriavidus gilardii is an emerging multidrug-resistant pathogen found in many environments and few clinical samples. The clinical infectiousness, pathogenicity, and resistance mechanisms of C. gilardii are still unclear due to the lack of clinical and sequencing data. We need to obtain insight into the clinical characteristics, virulence, and resistance mechanisms of C. gilardii.

Patients and Methods

We isolated five C. gilardii isolates from hospitalized patients and carried out assay, culture and genome sequencing. We analyzed the genomic features of clinical C. gilardii isolates and took insight into their clinical characteristics, virulence, and resistance mechanisms.

Results

These isolates were resistant to meropenem, gentamicin, and other antimicrobials due to intrinsic resistance genes. Furthermore, the sequencing results revealed the widespread presence of the MCR-5.1 gene in C. gilardii. The virulence magnitude of C. gilardii is closely correlated with the number of virulence factors they carry. Some C. gilardii strains can acquire resistance to levofloxacin through gyrA gene mutation during treatment. The diverse antimicrobial resistance mechanisms challenge the treatment of C. gilardii infections.

Conclusion

We present the genomic characteristics of clinically isolated C. gilardii to improve (i) our understanding of this pathogen and (ii) treatment options.

Heavy metal-tolerant bacteria Bacillus cereus BCS1 degrades pyrethroid in a soil-plant system

The heightened concern about the environmental impacts of pollutants drives interest in reducing their threats to humans and the environment. Bioremediating polluted sites under environmental stresses like biotic and abiotic poses significant challenges. This study aimed to isolate a bacterium that effectively degrades pyrethroids even under abiotic stresses involving heavy metals and biotic stresses with autochthonous factors. Here, a bacterial strain, Bacillus cereus BCS1 was isolated. The response surface methodology was established to quantify the environmental impacts on pyrethroid degradation. BCS1 effectively degraded pyrethroids across conditions at 21-36 °C, pH 6.5-8.0 and inoculum sizes 1.9-4.1 mg·L-1, exceeding 90% degradation. Notably, over 84% of β-cypermethrin (β-CP) was degraded even when exposed to various concentrations of lead (10-1000 mg·L-1), chromium (10-1000 mg·L-1), or cadmium (0.5-50 mg·L-1). Moreover, BCS1 significantly accelerated β-CP degradation in soil-plant systems, displaying biotic stress tolerance, with lower half-life values (10.1 and 9.5 d) in soil and higher removal (92.1% and 60.9%) in plants compared to controls (27.7 and 25.7 d), and (18.2% and 24.3%). This study presents a novel strain capable of efficiently degrading pyrethroids and displaying remarkable environmental stress resistance. Findings shed light on bioremediating organic pollutants in complex soil ecosystems.

Biomolecular insights into the inhibition of heavy metals on reductive dechlorination of 2,4,6-trichlorophenol in Pseudomonas sp. CP-1

Influences of heavy metal exposure to the organohalide respiration process and the related molecular mechanism remain poorly understood. In this study, a non-obligate organohalide respiring bacterium, Pseudomonas sp. strain CP-1, was isolated and its molecular response to the five types of commonly existed heavy metal ions were thoroughly investigated. All types of heavy metal ions posed inhibitory effects on 2,4,6-trichlorophenol dechlorination activity and cell growth with the varied degree. Exposure to Cu (II) showed the most serious inhibitive effects on dechlorination even at the lowest concentration of 0.05 mg/L, while the inhibition by As (V) was the least with the removal kinetic constant k decreased to 0.05 under 50 mg/L. Further, multi-omics analysis found compared with Cu (II), As (V) exposure led to the insignificant downregulation of a variety of biosynthesis processes, which would be one possible account for the less inhibited activity. More importantly, the inhibited mechanisms on the organohalide respiration catabolism of strain CP-1 were firstly revealed. Cu (II) stress severely downregulated NADH generation during TCA cycle and electron donation of organohalide respiration process, which might decrease the reducing power required for organohalide respiration. While both Cu (II) and As (Ⅴ) inhibited substrate level phosphorylation during TCA cycle, as well as electron transfer and ATP generation during organohalide respiration. Meanwhile, CprA-2 was confirmed as the responsible reductive dehalogenase in charge of 2,4,6-TCP dechlorination, and transcriptional and proteomic studies confirmed the directly inhibited gene transcription and expression of CprA-2. The in-depth reveal of inhibitory effects and mechanism gave theoretical supports for alleviating heavy metal inhibition on organohalide respiration activity in groundwater co-contaminated with organohalides and heavy metals.

The copper resistance mechanism in a newly isolated Pseudoxanthomonas spadix ZSY-33

Resolving the heavy metal resistance mechanisms of microbes is crucial for understanding the bioremediation of the ecological environment. In this study, a multiple heavy metal resistance bacterium, Pseudoxanthomonas spadix ZSY-33 was isolated and characterized. The copper resistance mechanism was revealed by analysis of the physiological traits, copper distribution, and genomic and transcriptomic data of strain ZSY-33 cultured with different concentrations of copper. The growth inhibition assay in basic medium showed that the growth of strain ZSY-33 was inhibited in the presence of 0.5 mM copper. The production of extracellular polymeric substances increased at a lower concentration of copper and decreased at a higher concentration of copper. Integrative analysis of genomic and transcriptomic, the copper resistance mechanism in strain ZSY-33 was elucidated. At a lower concentration of copper, the Cus and Cop systems were responsible for the homeostasis of intracellular copper. As the concentration of copper increased, multiple metabolism pathways, including the metabolism of sulfur, amino acids, and pro-energy were cooperated with the Cus and Cop systems to deal with copper stress. These results indicated a flexible copper resistance mechanism in strain ZSY-33, which may acquire from the long-term interaction with the living environment.

Comparative secretomic and proteomic analysis reveal multiple defensive strategies developed by Vibrio cholerae against the heavy metal (Cd2+, Ni2+, Pb2+, and Zn2+) stresses

Vibrio cholerae is a common waterborne pathogen that can cause pandemic cholera in humans. The bacterium with heavy metal-tolerant phenotypes is frequently isolated from aquatic products, however, its tolerance mechanisms remain unclear. In this study, we investigated for the first time the response of such V. cholerae isolates (n = 3) toward the heavy metal (Cd2+, Ni2+, Pb2+, and Zn2+) stresses by comparative secretomic and proteomic analyses. The results showed that sublethal concentrations of the Pb2+ (200 μg/mL), Cd2+ (12.5 μg/mL), and Zn2+ (50 μg/mL) stresses for 2 h significantly decreased the bacterial cell membrane fluidity, but increased cell surface hydrophobicity and inner membrane permeability, whereas the Ni2+ (50 μg/mL) stress increased cell membrane fluidity (p < 0.05). The comparative secretomic and proteomic analysis revealed differentially expressed extracellular and intracellular proteins involved in common metabolic pathways in the V. cholerae isolates to reduce cytotoxicity of the heavy metal stresses, such as biosorption, transportation and effluxing, extracellular sequestration, and intracellular antioxidative defense. Meanwhile, different defensive strategies were also found in the V. cholerae isolates to cope with different heavy metal damage. Remarkably, a number of putative virulence and resistance-associated proteins were produced and/or secreted by the V. cholerae isolates under the heavy metal stresses, suggesting an increased health risk in the aquatic products.

Decolorization potential of malachite green by Ralstonia mannitolilytica isolated from Indonesian cassava-based fermented food tapai

Pollution due to textile dye effluent mishandling is hazardous to ecosystems and to the living beings inhabiting them. This can cause retarded photosynthesis, disrupted fish day/night cycles, unbalanced bacterial populations, and decreased oxygen concentration in contaminated water, leading to low habitability. In this study, we aimed to isolate and characterize the microorganisms found in Indonesian cassava-based fermented food tapai starter cultures as a source of potential microbes for the biological remediation of textile dye pollutants. Microorganisms in the tapai starter culture were screened for their decolorization activity via spread-culture inoculation on a solid growth medium supplemented with textile dyes. Isolated microorganisms were selected based on their ability to secrete textile dye-decolorizing extracellular enzymes via increased light penetration after incubation of the cell-free supernatant (CFS) containing extracellular enzymes in textile dye solutions. Isolate JSP1 was the only bacterium capable of producing malachite green (MG)-decolorizing extracellular enzymes, which enabled it to survive and decolorize MG up to 375 ppm. Moreover, isolate JSP1 CFS was able to optimally decolorize 75% of MG at 100 ppm, but its activity was diminished at concentrations > 350 ppm. Colony and cellular morphology, biochemistry, and 16S rRNA tests revealed that the isolate was of Ralstonia mannitolilytica. Therefore, R. mannitolilytica isolate JSP1 may be a potential bioremediation agent for MG.

Comparative metabolomic analysis reveals Ni(II) stress response mechanism of Comamonas testosteroni ZG2

The focus on the toxicity of nickel (Ni(II)) in animal and human cells has increased recently. Ni(II) contamination hazards to animals and humans can be reduced by bioremediation methods. However, one of the limitation of bioremediation bacteria in soil remediation is that they cannot survive in moderate and heavy contamination Ni(II)-contaminated environments. Therefore, the Ni(II) response mechanism of Comamonas testosteroni ZG2 which has soil remediation ability in high-concentration Ni(II) environment must be elucidated. The results demonstrated that the ZG2 strain can survive at 350 mg/L concentration of Ni(II), but the growth of ZG2 was completely inhibited under the concentration of 400 mg/L Ni(II) with significant alterations in the membrane morphology, adhesion behavior, and functional groups and serious membrane damage. Furthermore, the metabolic analysis showed that Ni(II) may affect the adhesion behavior and biofilm formation of the ZG2 strain by affecting the abundance of metabolites in amino acid biosynthesis, aminoacyl-tRNA biosynthesis, ABC transporter, and cofactor biosynthesis pathways, and inhibiting its growth. This study provides new evidence clarifying the response mechanism of Ni(II) stress in the ZG2 strain, thus playing a significant role in designing the strategies of bioremediation.

The Facile Synthesis of Eco-Friendly Zinc Magnesium Bimetal Nanoparticles and its Application in the Eradication of Xanthomonas oryzae pv. oryzae that Causes Leaf Blight Disease of Rice

In this research work, we formulated and successfully assessed the antibacterial capability of zinc magnesium bimetal nanoparticles (ZnMgNPs) against Xanthomonas oryzae pv. oryzae (Xoo), the pathogenic microorganism responsible for causing the destructive leaf blight disease in rice. Successful preparation of ZnMgNPs were determined by UV-vis spectroscopy, EDX (Energy dispersive X-ray), FTIR (Fourier transform infrared) and SEM (Scanning Electron Microscopy). ZnMgNPs had antibacterial efficacy towards Xoo at MIC (minimum inhibitory concentration) 50 µg/ml. ZnMgNPs impeded the formation of biofilm of Xoo by drastically reducing the amount of EPS (extracellular polymeric substances) production and number of sessile cells. The ZnMgNPs also reduced several pathogenic traits of Xoo like motility, xanthomonadin and exoenzymes production. ZnMgNPs target cell membrane of Xoo and also induced oxidative damage as mechanisms of its antibacterial activity. As revealed by an ex-vivo study, ZnMgNPs diminished BLB (bacterial leaf blight) disease symptoms in rice leaves, ZnMgNPs had no effect on rice seed germination, and that following foliar application, the length and biomass of roots and shoots of rice seedling were unaffected, low cytotoxic to A549 cell line showing that ZnMgNPs are non-toxic. However, with ZnMgNPs treatment, the chlorophyll content index (CCI) increased significantly, indicating a good impact on rice physiology. All of these findings suggest that ZnMgNPs could be applied in agriculture to combat the Xoo-caused BLB disease.

Cr(VI) Reduction and Fe(II) Regeneration by Penicillium oxalicum SL2-Enhanced Nanoscale Zero-Valent Iron

Nanoscale zero-valent iron (nZVI) faces significant challenges in Cr(VI) remediation through aggregation and passivation. This study identified a Cr(VI)-resistant filamentous fungus (Penicillium oxalicum SL2) for nZVI activation and elucidated the synergistic mechanism in chromium remediation. P. oxalicum SL2 and nZVI synergistically and effectively removed Cr(VI), mainly by extracellular nonenzymatic reduction (89.1%). P. oxalicum SL2 exhibited marked iron precipitate solubilization and Fe(II) regeneration capabilities. The existence of the Fe(II)-Cr(V)-oxalate complex (HCrFeC₄O₉) indicated that in addition to directly reducing Cr(VI), iron ions generated by nZVI stimulated Cr(VI) reduction by organic acids secreted by P. oxalicum SL2. RNA sequencing and bioinformatics analysis revealed that P. oxalicum SL2 inhibited phosphate transport channels to suppress Cr(VI) transport, facilitated iron and siderophore transport to store Fe, activated the glyoxylate cycle to survive harsh environments, and enhanced organic acid and riboflavin secretion to reduce Cr(VI). Cr(VI) exposure also stimulated the antioxidative system, promoting catalase activity and maintaining the intracellular thiol/disulfide balance. Cr(VI)/Fe(III) reductases played crucial roles in the intracellular reduction of chromium and iron, while nZVI decreased cellular oxidative stress and alleviated Cr(VI) toxicity to P. oxalicum SL2. Overall, the P. oxalicum SL2-nZVI synergistic system is a promising approach for regenerating Fe(II) while reducing Cr(VI).

Bacillus coagulans XY2 ameliorates copper-induced toxicity by bioadsorption, gut microbiota and lipid metabolism regulation

Excessive copper pollutes the environment and endangers human health, attracting plenty of global attention. In this study, a novel strain named Bacillus coagulans XY2 was discovered to have a great copper tolerance and adsorption capacity. B. coagulans XY2 might maintain copper homeostasis through multisystem synergies of copper resistance, sulfur metabolism, Fe-S cluster assembly, and siderophore transport. In mice, by promoting the expression of SREBF-1 and SREBF-2 and their downstream genes, B. coagulans XY2 significantly inhibited the copper-induced decrease in weight growth rate, ameliorated dyslipidemia, restored total cholesterol and triglyceride contents both in serum and liver. Furthermore, B. coagulans XY2 recovered the diversity of gut microbiota and suppressed the copper-induced reduction in the ratio of Firmicutes to Bacteroidota. Serum metabolomics analysis showed that the alleviating effect of B. coagulans XY2 on copper toxicity was mainly related to lipid metabolism. For the first time, we demonstrated mechanisms of copper toxicity mitigation by B. coagulans XY2, which was related to self-adsorption, host copper excretion promotion, and lipid metabolism regulation. Moreover, working model of B. coagulans XY2 on copper homeostasis was predicted by whole-genome analysis. Our study provides a new solution for harmfulness caused by copper both in human health and the environment.

Microbial induced phosphate precipitation accelerate lead mineralization to alleviate nucleotide metabolism inhibition and alter Penicillium oxalicum's adaptive cellular machinery

Microbial-induced phosphate (P) precipitation (MIPP) based on P-solubilizing microorganisms (PSM) is regarded as a promising approach to bioimmobilize environmental lead (Pb). Nevertheless, the underlying changes of Pb²⁺ biotoxicity in PSM during MIPP process were rarely discussed. The current study explored the Pb²⁺ immobilization and metabolic changes in PSM Penicillium oxalicum postexposure to Pb²⁺ and/or tricalcium phosphate (TCP). TCP addition significantly increased soluble P concentrations, accelerated extracellular Pb mineralization, and improved antioxidative enzyme activities in P. oxalicum during MIPP process. Secondary Pb²⁺ biomineralization products were measured as hydroxypyromorphite [Pb₁₀(PO₄)₆(OH)₂]. Using untargeted metabolomic and transcriptomics, we found that Pb²⁺ exposure stimulated the membrane integrity deterioration and nucleotide metabolism obstruction of P. oxalicum. Correspondingly, P. oxalicum could produce higher levels of gamma-aminobutyric acid (GABA) to enhance the adaptive cellular machineries under Pb²⁺ stress. While the MIPP process improved extracellular Pb²⁺ mineralization, consequently alleviating the nucleotide metabolism inhibition and membrane deterioration. Multi-omics results suggested that GABA degradation pathway was stimulated for arginine biosynthesis and TCA cycle after Pb²⁺ mineralization. These results provided new biomolecular information underlying the Pb²⁺ exposure biotoxicities to microorganisms in MIPP before the application of this approach in environmental Pb²⁺ remediation.

Resistance properties and adaptation mechanism of cadmium in an enriched strain, Cupriavidus nantongensis X1T

Bacterial adaption to heavy metal stress is a complex and comprehensive process of multi-response regulation. However, the mechanism is largely unexplored. In this study, cadmium (Cd) resistance and adaptation mechanism in Cupriavidus nantongensis X1^T were investigated. Strain X1^T could resist the stress of 307 mg/L Cd²⁺ and remove 70% Cd²⁺ in 48 h. Spectroscopic analyses suggested interactions between Cd²⁺ with C-N, -COOH, and -NH ligands of extracellular polymeric substances. Whole-genome sequencing found that the resistance of Cd²⁺ in strain X1^T was caused by the joint action of Czc and Cad systems. Cd²⁺ at 20 mg/L elicited differential expression of 1157 genes in strain X1^T. In addition to the reported effects of uptake, adsorption, effluxion, and accumulation system, the oxidative stress system, Type-VI secretory protein system, Fe-S protein synthesis, and cysteine synthesis system in strain X1^T were involved in the Cd²⁺ resistance and accumulation. The intracellular accumulation content of Cd²⁺ in strain X1^T was higher than the extracellular adsorption content made strain X1^T to be an important resource strain in the bioremediation of Cd-contaminated sewage. The results provide a theoretical network for understanding the complex regulatory system of bacterial resistance and adaptation of Cd against stressful environments.

Comparative genome and transcriptome of Rhodococcus pyridinivorans GF3 for analyzing the detoxification mechanism of anthraquinone compounds

Anthraquinone compounds (ACs) could be efficiently degraded and detoxified by bacteria. However, the molecular mechanism of bacterial degradation and detoxification of ACs remains unclear. In this study, 1-aminoanthraquinone-2-sulfonate (ASA-2) was used as a model anthraquinone compound, the response mechanism of Rhodococcus pyridinivorans GF3 to ASA-2 using genomics and transcriptomics techniques was investigated. Comparative genome analysis showed that strain GF3 owned an especial gene region (Genes 1337-1399) containing the genes encoding cytochrome P450, monooxygenase, dehydrogenase and oxidoreductase, which did not commonly exist in Rhodococcus genus. The amino acid sequences of these genes were similar to those of the cleavage enzymes of anthraquinone ring in Aspergillus genus. Moreover, the transcriptions of Genes 1392-1394 (cytochrome 450 gene cluster) displayed 1.8-3.1-fold up-regulation under ASA-2 exposure. Meanwhile, as an intermediate product of ASA-2, catechol was degraded to acetyl-CoA, succinyl-CoA and pyruvate, resulting in the enhanced tricarboxylic acid cycle and ATP generation. This process also promoted the up-regulation of the genes encoding resistance, efflux, transporter and anti-oxidation pressure proteins, which were involved in resisting ASA-2 and maintaining the homeostasis of cells. These results provided us with a further understanding of the molecular mechanism of degradation and detoxification of ACs.

Response mechanism of psychrotolerant Bacillus cereus D2 towards Ni (II) toxicity and involvement of amino acids in Ni (II) toxicity reduction

The toxic effect of Nickel (Ni (II)) on humans and animals has been previously addressed. Owing to the important application of psychrotolerant bacteria in Ni (II) damage remediation in contamination sites at low temperatures, the response mechanism of psychrotolerant bacteria to Ni (II) toxicity must be elucidated. Therefore, the effect of Ni (II) toxicity on a psychrotolerant Bacillus cereus D2 was studied, showing a way to alleviate the Ni (II) toxicity in strain D2. The results showed that strain D2 growth was completely inhibited at a concentration of 100 mg/L of Ni (II). The main effects of Ni (II) toxicity on strain D2 were membrane damage and reactive oxygen species-dependent oxidative stress. Additionally, Ni (II) toxicity resulted in dysregulation of the cell cycle in strain D2. Furthermore, metabolomic analysis showed that the biosynthesis of amino acids and ABC transporters were significantly affected, and the relative abundance of seven important amino acids changed in a concentration-dependent manner. Addition of 20 mM or 5 mM amino acids to 100 mg/L Ni (II)-treated strain D2 restored its growth. This study provides insights into the way to alleviate the Ni (II) toxicity in strain D2, thus contributing to the development of bioremediation strategies.

Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress

It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation.

IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.

Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics

Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.4% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.

Mechanistic study of antimonate reduction by Escherichia coli W3110

Microbial-assisted antimonate [Sb(V)] reduction immobilizes this redox-sensitive metalloid in the subsurface. Most indigenous aerobes in antimony (Sb)-contaminated areas do not contain Sb(V)-reducing genes but can resist high levels of Sb(V) threat. Herein, to unravel the mechanisms of Sb(V) resistance by aerobes, we used Escherichia coli W3110 as a model aerobe and incubated it with 10 μM Sb(V). We found that strain W3110, without known Sb(V)-reducing genes, was able to reduce Sb(V) to Sb(III). Our transcriptome analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) results show that the Sb(V) threat at the 10 μM level had a negligible effect on the gene expression of strain W3110. In vitro incubation experiments further indicate that Sb(V) reduction was attributable to extracellular polymeric substances (EPS). Moreover, the three-dimensional excitation-emission matrix fluorescence spectroscopy reveals that the tryptophan-like components in EPS were involved in Sb(V) binding as evidenced by its weakened fluorescence intensity upon Sb(V) addition. The FTIR and XPS analyses indicate that hemiacetal and amide groups in EPS contributed to the reduction of Sb(V). Preculture with 10 μM Sb(V) did not exhibit a significant difference in Sb(V)-reducing capacity, suggesting that Sb(V) stress probably did not stimulate EPS secretion of W3110. Our results highlight the importance of EPS as the first line of defense against toxins, especially for those bacteria without such functional genes.

Transcriptome Analysis of Environmental Pseudomonas Isolates Reveals Mechanisms of Biodegradation of Naphthenic Acid Fraction Compounds (NAFCs) in Oil Sands Tailings

Naphthenic acid fraction compounds (NAFCs) are highly recalcitrant constituents of oil sands tailings. Although some microorganisms in the tailings can individually and synergistically metabolize NAFCs, the biochemical mechanisms that underpin these processes are hitherto unknown. To this end, we isolated two microorganisms, Pseudomonas protegens and Pseudomonas putida, from oils sands tailings and analyzed their transcriptomes to shed light on the metabolic processes employed by them to degrade and detoxify NAFCs. We identified 1048, 521 and 1434 genes that are upregulated in P. protegens, P. putida and a 1:1 co-culture of the strains, respectively. We subsequently enumerated the biochemical activities of enriched genes and gene products to reveal the identities of the enzymes that are associated with NAFC degradation. Separately, we analyzed the NAFCs that are degraded by the two pseudomonads and their 1:1 co-culture and determined the composition of the molecules using mass spectrometry. We then compared these molecular formulas to those of the cognate substrates of the enriched enzymes to chart the metabolic network and understand the mechanisms of degradation that are employed by the microbial cultures. Not only does the consortium behave differently than the pure cultures, but our analysis also revealed the mechanisms responsible for accelerated rate of degradation of NAFCs by the co-culture. Our findings provide new directions for engineering or evolving microorganisms and their consortia for degrading NAFCs more stably and aggressively.

Transcriptomic analysis reveals resistance mechanisms of Klebsiella michiganensis to copper toxicity under acidic conditions

The aim of this study was to elucidate the effect of pH on bacterial resistance mechanisms to copper (Cu) stress by genomic and transcriptomic analysis. Klebsiella michiganensis cells were exposed to 0.5 mM CuCl₂ at pH 4 and 5. Lower pH (pH < 4) strongly inhibited K. michiganensis growth, while Cu stress and higher pH (pH > 5) induced Cu precipitation in the medium. Transcriptomic analyses indicated that two groups of genes related to quorum sensing (QS) systems (lsrABCDFGKR) and type II secretion systems (T2SS) (gspCDEFGHIJKLM) were significantly up-regulated at pH 4 only. These results suggest that T2SS may be induced and controlled by QS, thereby contributing to the formation of extracellular polymeric substances (EPS) and the secretion of proteins to prevent Cu ions from entering cells. Six Cu resistance genes (cusABF, copA, cueO, and gene05308) were more significantly up-regulated at pH 4 than at pH 5. In addition, the relative expression (log₂|FC=) of the sulfur assimilation genes cysHJIK was relatively higher at pH 4 than at pH 5, while the gene encoding organic sulfur metabolism, tauB, was also significantly up-regulated at only pH 4. These results indicate that the Cu efflux system can remove intracellular Cu ions from cells, and that the sulfur assimilation system is related to the detoxification of Cu ions. Furthermore, increased free Cu ions at lower pH (4) could induce communication signals among cells, thereby stimulating the response of T2SS-related genes in K. michiganensis to tolerate Cu stress. Consequently, the resistance of K. michiganensis to Cu stress is a multisystem collaborative process composed of intracellular and extracellular components.

Transcriptomic analyses reveal the pathways associated with the volatilization and resistance of mercury(II) in the fungus Lecythophora sp. DC-F1

The biotic enzymatic reduction of mercury II [Hg(II)] to elemental Hg [Hg(0)] is an important pathway for Hg detoxification in natural ecosystems. However, the mechanisms of Hg(II) volatilization and resistance in fungi have not been understood completely. In the present study, we investigated the mechanisms of Hg(II) volatilization and resistance in the fungus Lecythophora sp. DC-F1. Hg(II) volatilization occurred during the investigation via the reduction of Hg(II) to Hg(0) in DC-F1. Comparative transcriptome analyses of DC-F1 revealed 3439 differentially expressed genes under 10 mg/L Hg(II) stress, among which 2770 were up-regulated and 669 were down-regulated. Functional enrichment analyses of genes and pathways further suggested that the Hg(II) resistance of DC-F1 is a multisystem collaborative process with three important transcriptional responses to Hg(II) stress: a mer-mediated Hg detoxification system, a thiol compound metabolism, and a cell reactive oxygen species stress response system. The phylogenetic analysis of merA protein homologs suggests that the Hg(II) reduction by merA is widely distributed in fungi. Overall, this study provides evidence for the reduction of Hg(II) to Hg(0) in fungi via the mer-mediated Hg detoxification system and offers a comprehensive explanation for its role within Hg biogeochemical cycling. These findings offer a strong theoretical basis for the application of fungi in the bioremediation of Hg-contaminated envionments.

The bioremediation potentials and mercury(II)-resistant mechanisms of a novel fungus Penicillium spp. DC-F11 isolated from contaminated soil

Bioremediation of Hg-contaminated soil using microbe-based strategies is a promising and efficient method as it is inexpensive and not harmful to the environment. In this study, a novel Hg(II)-volatilizing fungus Penicillium spp., DC-F11 was isolated and showed bioremediation potential for reducing Hg(II) phytotoxicity, total Hg, and exchangeable Hg in Hg(II)-polluted soil. Subsequently, the mechanisms of Hg(II) volatilization and resistance involved were investigated using multiple complementary techniques. The fungal cells could detoxify Hg(II) by extracellular sequestration via adsorption and precipitation. Moreover, a comparative transcriptome analysis uncovered the primary intracellular adaptive responses of the DC-F11 to Hg(II) stress, including mer-mediated detoxification system, thiol compound metabolism, and oxidative stress defense and damage repair metabolism. These results showed that the resistance of DC-F11 to Hg(II) was generally a multisystem collaborative process. Here, we report, for the first time, that the mer-mediated detoxification system was responsible for Hg(II) volatilization in fungus. These findings provide a better understanding of the mechanisms involved in Hg(II) volatilization and resistance that occur in fungi and also provide a strong theoretical basis for the future application of fungi in the bioremediation of Hg-polluted environments.

The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

Multifunctional molybdenum disulfide-copper nanocomposite that enhances the antibacterial activity, promotes rice growth and induces rice resistance

Molybdenum disulfide sheets loaded with copper nanoparticles (MoS₂-CuNPs) was prepared and its antibacterial activity against phytopathogen Xanthomonas oryzae pv. oryzae (Xoo) was investigated in vitro and in vivo for the first time. In a 2 h co-incubation, MoS₂-CuNPs exhibited 19.2 times higher antibacterial activity against Xoo cells than a commercial copper bactericide (Kocide 3000). In the detached leaf experiment, the disease severity decreased from 86.25 % to 7.5 % in the MoS₂-CuNPs treated rice leaves. The results further demonstrated that foliar application of MoS₂-CuNPs could form a protective film and increase the density of trichome on the surface of rice leaves, finally prevent the infection of Xoo cells. This was probably due to the synergistic effect of MoS₂-CuNPs. Additionally, foliar application of MoS₂-CuNPs (4-32 μg/mL) increased obviously the content of Mo and chlorophyll (up 30.85 %), and then improved the growth of rice seedlings. Furthermore, the obtained MoS₂-CuNPs could activate the activities of the antioxidant enzymes in rice, indicating higher resistance of rice under abiotic/biotic stresses. The multifunctional MoS₂-CuNPs with superior antibacterial activity provided a promising alternative to the traditional antibacterial agents and had great potential in plant protection.