Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus

Response of anammox consortia to inhibition from high ferroferric oxide nanoparticles concentration and potential recovery mechanism

The substantial discharge of ferroferric oxide nanoparticles (Fe3O4 NPs) into sewage threatens the survival of functional microorganisms in wastewater treatment. This study elucidated responses of anaerobic ammonium oxidation (anammox) consortia to inhibition from high Fe3O4 NPs concentration and recovery mechanisms. The nitrogen removal efficiency decreased by 20.3 % and recovered after 55 days under 1000 mg/L Fe3O4 NPs concentration. Toxicity was attributed to reactive oxygen species (ROS) production. The excessive ROS damaged membrane integrity, nitrogen metabolism, and DNA synthesis, resulting in the inhibition of anammox bacteria activity. However, recovery mechanisms of anammox consortia activity were activated in response to 1000 mg/L Fe3O4 NPs. The increase of heme oxygenase-1, thioredoxin, and nicotinamide adenine dinucleotide-quinone oxidoreductase genes alleviated oxidative stress. Furthermore, the activation of metabolic processes associated with membrane and DNA repair promoted recovery of anammox bacteria activity. This study provided new insights into NPs contamination and control strategies during anammox process.

Exploring the synergistic interplay of sulfur metabolism and electron transfer in Cr(VI) and Cd(II) removal by Clostridium thiosulfatireducens: Genomic and mechanistic insights

In this study, a sulfate-reducing bacterium, Clostridium thiosulfatireducens (CT) was reported and the performance and removal mechanism of Cr(VI) and Cd(II) removal were investigated. It is noteworthy that the dsrAB gene is absent in this strain, but the strain is capable of producing sulfide. The conversion rate of Cr(VI) by CT was 84.24 % at a concentration of 25 mg/L, and the conversion rate of Cd(II) was 94.19 % at a concentration of 28 mg/L. The complete genome is 6,106,624 bp and the genome consisted of a single chromosome. The GC content of the chromosomes was 29.65 %. The mechanism of heavy metal removal by CT bacteria mainly includes biosorption, electron transfer and redox, with reduction combined with S2- precipitation as the main pathway. The product characterization results showed that the formation of mainly ionic crystals and precipitates (CdS, Cd(OH)2, Cr(OH)3, Cr2O3) after adsorption. Genome-wide techniques have shown that the clearance of Cr(VI) and Cd(II) by CT is largely dependent on sulfate transport, sulfur metabolism, and energy metabolism to some extent. In addition, genes related to ATP binding, electron carrier activity, transporter protein genes, and DNA repair are also important factors to improve the heavy metal resistance and transformation ability of CT strains. Both the Fe-S cycle and the ROS-resistant system can enhance the electron transfer activity and thus slow down the damage of heavy metals to microorganisms. This study fills the gap in the understanding of the basic properties and heavy metal transformation mechanism of CT.

Shifts in bacterial diversity, interactions and microbial elemental cycling genes under cadmium contamination in paddy soil: Implications for altered ecological function

Cadmium (Cd) contamination has become an emergent environmental issue in agroecosystems worldwide. The impacts of Cd on microbial community and their ecological functional remain unrevealed. This study investigated the response of bacterial community and microbial ecological functions to Cd contamination in paddy soil of East China. Bacterial diversity and community structure significantly changed under Cd contamination. Proteobacteria and Acidobacteria were identified as biomarkers to indicate Cd contamination. The overall elemental cycling genes abundance was negatively correlated to soil Cd content. Acetyl-CoA synthesis, organic N mineralization, N fixation and nitrous reduction genes were especially sensitive to elevated Cd stress, resulting in loss of microbial derived soil C and N pool and increase in N2O emission potential. Bacteria interactions were sparser yet more competitive under Cd contamination. Cd resistant genera Massilia, Burkholderia, Streptomyces and Methylobacterium were essential to bacterial interactions via building connections with non-resistant species. Microbial Cd immobilization potential by urea hydrolysis was enhanced under Cd contamination, with Massilia being the keystone functional taxa involved in this process. Our study elucidated the ecological risks of altered microbial functions under Cd contamination in paddy soil, as well as the significance of Cd resistant bacteria to microbial community and ecological functionality.

Molecular fingerprint of gilthead seabream physiology in response to pollutant mixtures in the wild

The increase in trace element concentrations in the aquatic environment due to anthropogenic activities, urges the need for their monitoring and potential toxicity, persistence, bioaccumulation, and biomagnification at different trophic levels. Gilthead seabream is a species of commercial importance in the Mediterranean Sea, both for the aquaculture and fisheries sectors, however very little is known about their trace element contamination accumulation and the resulting effect on their health status. In the present study, 135 juveniles were collected from seven coastal lagoons known to be essential nursery areas for this species. We measured seventeen different inorganic contaminants at the individual level in fish muscle (namely Al, As, Be, Bi, Cd, Cr, Cu, Hg, Li, Ni, Pb, Rb, Sb, Sr, Ti, Tl and Zn). Our results revealed the accumulation of multiple trace elements in individuals and distinct contamination signatures between lagoons which might lead to contrasted quality as nurseries for juveniles of numerous ecologically and economically relevant fish species in addition to seabreams. We further evaluated the potential adverse effect of these complex contamination mixtures on the liver (the main organ implicated in the metabolism of xenobiotics) and red muscle (a highly metabolic organ) using a proteomic approach. Alterations in cellular organization pathways and protein transport were detected in both tissues (albeit they were not similarly regulated). Chromosome organization and telomere maintenance in the liver appeared to be affected by contaminant mixture which could increase mortality, age-related disease risk and shorter lifetime expectancy for these juveniles. Red muscle proteome also demonstrated an upregulation of pathways involved in metabolism in response to contamination which raises the issue of potential energy allocation trade-offs between the organisms' main functions such as reproduction and growth. This study provides new insights into the cellular and molecular responses of seabreams to environmental pollution and proposed biomarkers of health effects of trace elements that could serve as a starting point for larger-scale biomonitoring programs.

The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development

A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer-binding protein (bEBP) NtrC and its cognate sensor histidine kinase, NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of Caulobacter crescentus ntrC slows cell growth in complex medium and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC-binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid-associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter. IMPORTANCE Bacteria balance cellular processes with the availability of nutrients in their environment. The NtrB-NtrC two-component signaling system is responsible for controlling nitrogen assimilation in many bacteria. We have characterized the effect of ntrB and ntrC deletion on Caulobacter growth and development and uncovered a role for spontaneous IS element transposition in the rescue of transcriptional and nutritional deficiencies caused by ntrC mutation. We further defined the regulon of Caulobacter NtrC, a bacterial enhancer-binding protein, and demonstrate that it shares specific binding sites with essential proteins involved in cell cycle regulation and chromosome organization. Our work provides a comprehensive view of transcriptional regulation mediated by a distinctive NtrC protein, establishing its connection to nitrogen assimilation and developmental processes in Caulobacter.

The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development

A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer binding protein (bEBP) NtrC, and its cognate sensor histidine kinase NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of C. crescentus ntrC slows cell growth in complex medium, and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter .

Physiological and transcriptional studies reveal Cr(VI) reduction mechanisms in the exoelectrogen Cellulomonas fimi Clb-11

A facultative exoelectrogen, Cellulomonas fimi strain Clb-11, was isolated from polluted river water. This strain could generate electricity in microbial fuel cells (MFCs) with carboxymethyl cellulose (CMC) as the carbon source, and the maximum output power density was 12.17 ± 2.74 mW·m^-2. In addition, Clb-11 could secrete extracellular chromate reductase or extracellular electron mediator to reduce Cr(VI) to Cr(III). When the Cr(VI) concentration was less than 0.5 mM in Luria-Bertani (LB) medium, Cr(VI) could be completely reduced by Clb-11. However, the Clb-11 cells swelled significantly in the presence of Cr(VI). We employed transcriptome sequencing analysis to identify genes involved in different Cr(VI) stress responses in Clb-11. The results indicate that 99 genes were continuously upregulated while 78 genes were continuously downregulated as the Cr(VI) concentration increased in the growth medium. These genes were mostly associated with DNA replication and repair, biosynthesis of secondary metabolites, ABC transporters, amino sugar and nucleotide sugar metabolism, and carbon metabolism. The swelling of Clb-11 cells might have been related to the upregulation of the genes atoB, INO1, dhaM, dhal, dhak, and bccA, which encode acetyl-CoA C-acetyltransferase, myo-inositol-1-phosphate synthase, phosphoenolpyruvate-glycerone phosphotransferase, and acetyl-CoA/propionyl-CoA carboxylase, respectively. Interestingly, the genes cydA and cydB related to electron transport were continuously downregulated as the Cr(VI) concentration increased. Our results provide clues to the molecular mechanism of Cr(VI) reduction by microorganisms in MFCs systems.

Genetic mechanisms for Se(VI) reduction and synthesis of trigonal 1-D nanostructures in Stenotrophomonas bentonitica: Perspectives in eco-friendly nanomaterial production and bioremediation

Selenate (Se(VI)) is one of the most soluble and toxic species of Se. Microbial Se(VI) reduction is an efficient tool for bioremediation strategies. However, this process is limited to a few microorganisms, and its molecular basis remains unknown. We present detailed Se(VI)-resistance mechanisms under 50 and 200 mM, in Stenotrophomonas bentonitica BII-R7, coupling enzymatic reduction of Se(VI) to formation of less toxic trigonal Se (t-Se). The results reveal a concentration-dependent response. Despite the lack of evidence of Se(VI)-reduction to Se(0) under 50 mM Se(VI), many genes were highly induced, indicating that Se(VI)-resistance could be based on intracellular reduction to Se(IV), mainly through molybdenum-dependent enzymes (e.g. respiratory nitrate reductase), and antioxidant activity by enzymes like glutathione peroxidase. Although exposure to 200 mM provoked a sharp drop in gene expression, a time-dependent process of reduction and formation of amorphous (a), monoclinic (m) and t-Se nanostructures was unravelled: a-Se nanospheres were initially synthesized intracellularly, which would transform into m-Se and finally into t-Se nanostructures during the following phases. This is the first work describing an intracellular Se(VI) reduction and biotransformation process to long-term stable and insoluble t-Se nanomaterials. These results expand the fundamental understanding of Se biogeochemical cycling, and the effectiveness of BII-R7 for bioremediation purposes.

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

Isolation of heavy metal-resistant Staphylococcus epidermidis strain TWSL_22 and evaluation of heavy metal bioremediation potential of recombinant E. coli cloned with isolated cadD

A heavy metal-resistant bacterial strain, TWSL_22 was isolated from an industrial effluent sample and tested for heavy metal tolerance and resistance. The strain was molecularly characterized as Staphylococcus epidermidis based on 16S rDNA gene analysis and the sequence was deposited in the NCBI repository (accession number KT184893.1). Metal removal activity (P < .001) of TWSL_22 was 99.99 ± 0.001%, 74.43 ± 2.51%, and 51.16 ± 4.17% for Cd, Pb, and Cu, respectively. Highest MIC was observed for Cd. Antibiotic susceptibility assays revealed the strain TWSL_22 to be resistant to several antibiotics. The strain was screened for possible heavy metal-resistant genes and presence of cadA, copA, and cadD was confirmed by PCR. A DNA fragment containing complete sequence of cadD (618 bp) was isolated and cloned into pET 21a(+), transformed into E. coli BL21 and designated as E. coli/cadDET. E. coli/cadDET showed high metal tolerance capacity and could remove over 82% of heavy metals (Zn2+, Cd2+, Cu2+, and Cr3+) in the industrial effluent.

Physiological, biochemical, and genomic elucidation of the Ensifer adhaerens M8 strain with simultaneous arsenic oxidation and chromium reduction

This study reports the simultaneous oxidation of As(III) and reduction of the Cr(VI) strain Ensifer adhaerens M8 screened from soils around abandoned gold tailings contaminated with highly complex metals (loids). Physiological, biochemical, and genomic techniques were used to explore the mechanism. The strain M8 could simultaneously oxidize 1 mM As(III) and reduce 45.3 % 0.1 mM Cr(VI) in 16 h, and the Cr(VI) reduction rate was increased by 5.8 % compared with the addition of Cr(VI) alone. Cellular debris was the main site of M8 arsenic oxidation. Chromium reduction was dominated by the reduction of extracellular hexavalent chromium (23.80-35.67 %). The genome of M8 included one chromosome and four plasmids, and a comparison of the genomes showed that M8 had two more plasmids than strains of the same genus, which may be related to strong environmental adaptations. M8 had 10 heavy metal resistance genes (HMRs), and plasmid D had a complete cluster of arsenic resistance-oxidation-transport genes (arsOHBCCR-aioSR-aioBA-cytCmoeA-phoBBU-PstBACS-phnCDEE). The genes involved in Cr(VI) detoxification include DNA repair (RecG, ruvABC, and UvrD), Cr(VI) transport (chrA, TonB, and CysAPTW) and Cr(VI) reduction. In summary, this study provides a molecular basis for As (III) and Cr (VI) remediation.

Soybean rhizosphere microorganisms alleviate Mo nanomaterials induced stress by improving soil microbial community structure

With the wide application of nanomaterials (NMs) in agriculture, it is particularly important to assess the impact of these NMs on soil microorganisms. In this study, different varieties of soybean rhizosphere microorganisms (RM) were employed to simulate the alleviate effect of molybdenum nanoparticles (Mo NPs) induced stress in presence of soybean plants. Mo NPs caused serious toxic effects on soybean growth and nitrogen fixation at a concentration of 100 mg kg^-1: plant height and biomass were reduced by 56.4% and 82.8%, respectively, and the ability to fix nitrogen was almostly lost. However, after adding different varieties of soybean RM (RM-Williams 82, RM-Youchun 1204, and RM-Zhongdou 41), the stress caused by high concentrations of Mo NPs on soybean plants was significantly reduced. The plant height, root length, biomass, and nitrogen fixation ability were improved by 70.8%, 80.7%, 145.8%, and 349.8%, respectively, following the addition of soybean RM-Williams 82. High-throughput sequencing revealed that Mo NPs treatment affected the microbial community structure. Among them, Flavisolibacter and Caulobacter genera abundance increased significantly, which might be the key factor in relieving Mo NPs-induced stress on soybean growth. These findings suggest a novel mode of RM as a promising strategy to prevent deleterious effects of stress with NPs on plants in the future.

Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool

Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.

Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles

In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.

Characterization of the simultaneous degradation of pyrene and removal of Cr(VI) by a bacteria consortium YH

Microorganisms that can simultaneously remediate organic pollutants and heavy metal contamination are great significance in bioremediation. Nevertheless, reports of such microorganisms are still scarce. Here, Pseudomonas sp. YH-1 and Rhodococcus sp. YH-3 were isolated and identified, and they showed greater tolerance to hexavalent (VI) (750 and 800 mg·L^-1). The constructed bacteria consortium YH (YH-1:YH-3 = 1:1) could simultaneously degrade 41.69% of pyrene (50 mg·L^-1) and remove 76.67% of Cr(VI) (30 mg·L^-1) within 5 days. The potential mechanism of Cr(VI) tolerance of YH was further explored by genomic and microscopic analysis. The results showed that YH responded to Cr(VI) stress mainly through efflux of Cr(VI) by chrA and copZ, chromate reduction, DNA-repaired proteases reduces ROS damage, and biosorption by carboxyl, hydroxyl, amino functional groups. Strains YH-1 and YH-3 also contained a variety of genes associated with resistance to other heavy metals, such as cadmium (czcBD), mercury (merAPTR), manganese (mntABC) and copper (copAC, cusABRF and pcoBD). Based on GC-MS and genomic analysis, pyrene was degraded via salicylic acid and phthalic acid pathways. Moreover, a great number of genes related to aromatic hydrocarbon catabolism were identified in the genomes of YH-1 and YH-3. These results confirmed the potential application of the bacteria consortium YH in the bioremediation of water and soil co-contaminated with PAHs-heavy metals.

Effect of extracellular proteins on Cd(II) adsorption in fungus and algae symbiotic system

Fungus-algae symbiotic systems (FASS) are typically used to assist in the immobilization of algae and strengthen the adsorption of heavy metals. However, the adsorption behavior of the symbiotic system and the molecular regulation mechanism of extracellular proteins in the adsorption of heavy metals have not been reported in detail. In this study, a stable FCSS (fungus-cyanobacterium symbiotic system) was used to study Cd(II) adsorption behavior. The fixation efficiency of fungus to cyanobacterium reached more than 95% at pH7.0, 30 °C, 150 rpm, and a medium ratio of 100%. The biomass, chlorophyll content, and total fatty acid content of the symbiotic system were much higher than those of cyanobacterium and fungus alone. The photosynthetic fluorescence parameters showed that the presence of fungus enhanced the light tolerance of cyanobacterium. The original light energy conversion efficiency and potential activity of PSII were enhanced, indicating that symbiosis could promote the photosynthetic process of cyanobacterium. The Cd(II) adsorption efficiency can achieve 90%. The system maintained excellent adsorption after six adsorption cycles. Differential proteins were mainly enriched in areas such as metabolism, ABC transport system, and pressure response. Cd(II) stress promotes an increase in efflux proteins. Moreover, cadmium can be fixed as much as possible by secreting extracellular proteins, and the toxicity of cadmium to cells can be alleviated by regulating the metabolism of glutathione, reducing oxidative phosphorylation level, and reducing oxidative stress, thus improving the resistance to Cd(II). Meanwhile, the expression of enzymes involved in glycolysis and the pentose phosphate pathway was upregulated, while the expression of those in the TCA cycle was downregulated. The expression of substances related to PSI and PSII in the photosynthetic system and rubisco, a key enzyme in the Calvin cycle, was significantly upregulated, indicating that the glucose metabolism and photosynthetic pathways of the symbiotic system were involved in resistance to Cd toxicity. This revealed the response mechanism of the fungus-algal symbiotic system in the process of Cd adsorption, and also provided reference value for industrial application in water treatment.

Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota)

In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.

Biodegradation performance and diversity of enriched bacterial consortia capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are key organic pollutants in the environment that pose threats to the ecosystem and human health. The degradation of high molecular weight (HMW) PAHs by enriched bacterial consortia has been previously studied, while the involved metabolisms and microbial communities are still unclear and warrant further investigations. In this study, five bacterial consortia capable of utilizing different PAHs (naphthalene, anthracene, and pyrene) as the sole carbon and energy sources were enriched from PAH-contaminated soil samples. Among the five consortia, consortium TC exhibited the highest pyrene degradation efficiency (91%) after 19 d of incubation. The degradation efficiency was further enhanced up to 99% by supplementing yeast extract. Besides, consortium TC showed tolerances to high concentrations of pyrene (up to 1000 mg/L) and different heavy metal stresses (including Zn²⁺, Cd²⁺, and Pb²⁺). The dominant genus in consortium TC, GS, and PL showing relatively higher degradation efficiency for anthracene and pyrene was Pseudomonas, whereas consortium PG and GD were predominated by genus Achromobacter and class Enterobacteriaceae, respectively. Consortium TC, as a highly efficient HMW PAH-degrading consortium, could be applied for synergistic biodegradation of HMW PAHs and in situ bioremediation of the sites contaminated with both PAHs and heavy metals.

Exploration on the Cr(VI) resistance mechanism of a novel thermophilic Cr(VI)-reducing bacteria Anoxybacillus flavithermus ABF1 isolated from Tengchong geothermal region, China

Hexavalent chromium resistance and reduction mechanisms of microorganism provide a critical guidance for Cr(VI) bioremediation. However, related researches are limited in mesophiles and deficient for thermophiles. In this work, a novel alkaline Cr(VI)-reducing thermophile Anoxybacillus flavithermus ABF1 was isolated from geothermal region. The mechanisms of Cr(VI) resistance and reduction were investigated. The results demonstrated that A. flavithermus ABF1 could survive in a wide temperature range from 50°C to 70°C and in pH range of 7.0-9.0. Strain ABF1 showed excellent growth activity and Cr(VI) removal performance when initial Cr(VI) concentration was lower than 200 mg L^-1 . 93.71% of Cr(VI) was removed at initial concentration of 20 mg L^-1 after 72 h. The majority of Cr(VI) was found to be reduced extracellularly by enzymes secreted by cells. XPS and Raman analysis further manifested that Cr₂ O₃ was the product of Cr(VI) reduction. Moreover, the Cr(VI) transportation-related gene cysP and Cr(VI) reduction-related gene azoR of A. flavithermus ABF1 played key roles in inhibiting Cr(VI) entering cells and promoting extracellular Cr(VI) reduction respectively. This work provides novel insight into the mechanisms of Cr(VI) resistance and detoxication of thermophiles, which leads to a promising alternative strategy for heavy metal bioremediation in areas with elevated temperature.

Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium

Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. Cr13.

Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants

Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg²⁺, Zn²⁺, Pb²⁺, Au³⁺, Cd²⁺, As³⁺, Ni²⁺, Cu²⁺, and UO₂²⁺) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.

A systematic review on groundwater radon distribution with human health consequences and probable mitigation strategy

Groundwater radon contamination is a serious global concern for its eco-toxicological effects. The major health hazard occurs due to toxic indoor air inhalation and consumption of contaminated drinking water supplied from different distribution systems, especially groundwater. There are fragmented reports on the measurement of radon contamination and their health consequences with physical radon removal strategies as well as characterization of inhabitant microbial communities. As it concerned with human health, collective information is much essential on their groundwater distribution, their physicochemical properties and possible mitigation strategies, not done so far. In such prospect, this review summarizes the physicochemical properties of radon, their sources, global as well as Indian groundwater radon contamination scenario, health effects and inhabitant microbes along with their survival strategies. It also summarizes the physical radon removal techniques and especially emphasizes the microbes based bioremediation process as well as a combination of both as a future effective radon remediation process.

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

Background

Acidophilic microorganisms like Leptospirillum sp. CF-1 thrive in environments with extremely low pH and high concentrations of dissolved heavy metals that can induce the generation of reactive oxygen species (ROS). Several hypothetical genes and proteins from Leptospirillum sp. CF-1 are known to be up-regulated under oxidative stress conditions.

Results

In the present work, the function of hypothetical gene ABH19_09590 from Leptospirillum sp. CF-1 was studied. Heterologous expression of this gene in Escherichia coli led to an increase in the ability to grow under oxidant conditions with 5 mM K₂CrO₄ or 5 mM H₂O₂. Similarly, a significant reduction in ROS production in E. coli transformed with a plasmid carrying ABH19_09590 was observed after exposure to these oxidative stress elicitors for 30 min, compared to a strain complemented with the empty vector. A co-transcriptional study using RT-PCR showed that ABH19_09590 is contained in an operon, here named the “och” operon, that also contains ABH19_09585, ABH19_09595 and ABH19_09600 genes. The expression of the och operon was significantly up-regulated in Leptospirillum sp. CF-1 exposed to 5 mM K₂CrO₄ for 15 and 30 min. Genes of this operon potentially encode a NADH:ubiquinone oxidoreductase, a CXXC motif-containing protein likely involved in thiol/disulfide exchange, a hypothetical protein, and a di-hydroxy-acid dehydratase. A comparative genomic analysis revealed that the och operon is a characteristic genetic determinant of the Leptospirillum genus that is not present in other acidophiles.

Conclusions

Altogether, these results suggest that the och operon plays a protective role against chromate and hydrogen peroxide and is an important mechanism required to face polyextremophilic conditions in acid environments.

Identification of a Novel Chromate and Selenite Reductase FesR in Alishewanella sp. WH16-1

A ferredoxin protein (AAY72_06850, named FesR) was identified to associate with chromate [Cr(VI)] resistance in Alishewanella sp. WH16-1. FesR and its similar proteins were phylogenetically separated from other reductase families. Unlike the reported Cr(VI) and selenite [Se(IV)] reductases, two 4Fe-4S clusters and one flavin adenine dinucleotide (FAD) -binding domain were found in the FesR sequence. The experiment in vivo showed that the mutant strain ΔfesR had lost partial Cr(VI) and Se(IV) reduction capacities compared to the wild-type and complemented strains. Furthermore, overexpression in Escherichia coli and enzymatic tests in vitro showed FesR were involved in Cr(VI) and Se(IV) reduction. 4Fe-4S cluster in purified FesR was detected by ultraviolet-visible spectrum (UV-VIS) and Electron Paramagnetic Resonance (EPR). The Km values of FesR for Cr(VI) and Se(IV) reduction were 1682.0 ± 126.2 and 1164.0 ± 89.4 μmol/L, and the Vmax values for Cr(VI) and Se(IV) reduction were 4.1 ± 0.1 and 9.4 ± 0.3 μmol min^–1 mg^–1, respectively. Additionally, site-directed mutagenesis and redox potential analyses showed that 4Fe-4S clusters were essential to FesR, and FAD could enhance the enzyme efficiencies of FesR as intracellular electron transporters. To the best of our knowledge, FesR is a novel Cr(VI) and Se(IV) reductase.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO₂²⁺ and Fe³⁺. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.

Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey

Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

Cupriavidus metallidurans NA4 actively forms polyhydroxybutyrate-associated uranium-phosphate precipitates

Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 µM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uranium-phosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4.

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.

Highly efficient and sustainable removal of Cr (VI) in aqueous solutions by photosynthetic bacteria supplemented with phosphor salts

Photosynthetic bacteria have flexible metabolisms and strong environmental adaptability, and require cheap, but plentiful, energy supplements, which all enable their use in Cr(VI)-remediation. In this study, the effects of culture conditions on the total Cr removal rate were investigated for a newly identified strain of Rhodobacter sphaeroides SC01. The subcellular distribution and Cr(VI) reduction ability of four different cellular fractions were evaluated by scanning electron microscopy and transmission electron microscopy. Experiments indicated that the optimal culture conditions for total Cr removal included a culture temperature of 35 °C, pH of 7.20, an NaCl concentration of 5 g L^-1, a light intensity of 4000 lx, and an initial cell concentration (OD₆₈₀) of 0.15. In addition, most Cr was found in the cell membrane in the form of Cr (III) after reduction, while cell membranes had the highest Cr(VI) reduction rate (99%) compared to other cellular components. In addition, the physical and chemical properties of SC01 cells were characterized by FTIR, XPS, and XRD analyses, confirming that Cr was successfully absorbed on bacterial cell surfaces. CrPO₄‧6H₂O and Cr₅(P₃O₁₀)₃ precipitates were particularly identified by XRD analysis. After screening supplementation with five phosphor salts, Cr(VI) reduction due to bioprecipitation was improved by the addition of Na₄P₂O₇ and (NaPO₃)₆ salts, with the Cr(VI)-reduction rate combined with Na₄P₂O₇ addition being 15% higher than that of the control. Thus, this study proposes a new Cr(VI)-removal strategy based on the combined use of photosynthetic bacteria and phosphor salts, which importantly increases its potential application in treating wastewater.

Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics

To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea sp. strain MT58 (MT58), we used a multiomic strategy combining two global techniques, random bar code transposon site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al³⁺, the oxyanion CrO₄^2-, and the oxycation UO₂²⁺. Both global techniques were applied using all three metals under both aerobic and anaerobic conditions to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al³⁺ binds intracellular arginine, CrO₄^2- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO₂²⁺ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. Here, we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism, furthering our understanding of how living systems interact with their environment. IMPORTANCE Studying microbial interactions with their environment can lead to a deeper understanding of biological molecular mechanisms. In this study, two global techniques, RB-TnSeq and activity metabolomics, were successfully used to probe the interactions between a metal-resistant microorganism, Pantoea sp. strain MT58, and metals contaminating a site where the organism can be located. A number of novel metal-microbe interactions were uncovered, including Al³⁺ toxicity targeting arginine synthesis, which could lead to a deeper understanding of the impact Al³⁺ contamination has on microbial communities as well as its impact on higher-level organisms, including plants for whom Al³⁺ contamination is an issue. Using multiomic approaches like the one described here is a way to further our understanding of microbial interactions and their impacts on the environment overall.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Transcriptome analysis provides new insights into the tolerance and reduction of Lysinibacillus fusiformis 15-4 to hexavalent chromium

Microbial bioremediation of Cr(VI)-contaminated environments has drawn extensive concern. However, the molecular processes underlying the microbial Cr(VI) tolerance and reduction remain unclear. We isolated a Cr(VI)-reducing Lysinibacillus fusiformis strain 15-4 from soil on the Qinghai-Tibet Plateau. When grown in 1 mM and 2 mM Cr(VI)-containing medium, strain 15-4 could reduce 100% and 93.7% of Cr(VI) to Cr(III) after 36 h and 60 h of incubation, respectively. To know the molecular processes in response to Cr(VI), transcriptome sequencing was carried out using RNA-Seq technology. The results annotated a total of 3913 expressed genes in the strain. One thousand ninety-eight genes (28.1%) were significantly (fold change ≥ 2, false discovery rate ≤ 0.05) expressed in response to Cr(VI), of which 605 (55.1%) were upregulated and 493 (44.9%) were downregulated. The enrichment analysis showed that a total of 630 differentially expressed genes (DEGs) were enriched to 122 KEGG pathways, of which 8 pathways were significantly (p < 0.05) enriched in Cr(VI)-treated sample, including ATP-binding cassette (ABC) transporters (97 DEGs), ribosome (40), sulfur metabolism (16), aminoacyl-tRNA biosynthesis (19), porphyrin metabolism (20), quorum sensing (44), oxidative phosphorylation (17), and histidine metabolism (10), suggesting that these pathways play key roles to cope with Cr(VI) in the strain. The highly upregulated DEGs consisted of 29 oxidoreductase, 18 dehydrogenase, 14 cell redox homeostasis and stress response protein, and 10 DNA damage and repair protein genes. However, seven Na⁺:H⁺ antiporter complex-coding DEGs and most of transcriptional regulator-coding DEGs were significantly downregulated in the Cr-treated sample. Many of FMN/NAD(P)H-dependent reductase-encoding genes were greatly induced by Cr, suggesting the involvement of these genes in Cr(VI) reduction in strain 15-4. Sulfur and iron ions as well as the thiol-disulfide exchange reactions might play synergistic roles in Cr reduction.Key points• Lysinibacillus fusiformis 15-4 was able to tolerate and reduce Cr(VI) to Cr(III).• Transcriptome analysis revealed that 1098 DEGs and 8 key KEGG pathways significantly responded to Cr(VI).• Sulfur metabolism, protein biosynthesis, and porphyrin metabolism were the key pathways associated with the survival of strain 15-4 in response to Cr(VI).

Microbial reduction of Cr(VI) in the presence of Ni, Cu and Zn by bacterial consortium enriched from an electroplating contaminated site

The bioremediation of Cr(VI) has been intensively reported in recent years, while little information about Cr(VI)-reducing consortium enriched from in-situ contaminated soil has been revealed, specifically the functional genes involved. In this study, we verified a Cr(VI) reduction process by a consortium enriched from in-situ contaminated soil through enzymatic analysis. The chromate reductase gene ChrR has been successfully amplified and further analyzed, provided solid evidence to prove the Cr(VI) bio-reduction was an enzyme-mediated process. Meanwhile, the analysis of metabolic pathways demonstrates that the consortium could detoxicate and resist Cr(VI) and co-existing metals (Ni²⁺, Zn²⁺ and Cu²⁺) through membrane transport and DNA repair process. The co-existing heavy metals Zn and Cu had a relatively significant negative and positive effects on Cr(VI) reduction respectively, which may play important roles in the Cr(VI) contaminated soil bioremediation.

Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr

Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically and resists up 34 mM Cr(VI); this resistance is independent of the ChrA efflux transporter. In this study, we report the whole genome sequence and the transcriptional profile by RNA-Seq of strain AqSCr under Cr(VI)-adapted conditions and found 255 upregulated and 240 downregulated genes compared to controls without Cr(VI) supplementation. Genes differentially transcribed were mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid (FA) metabolism, ribosomal subunits, and energy metabolism. Among them, genes not previously associated with chromium resistance, for example, cybB, encoding a putative superoxide oxidase (SOO), gltA2, encoding an alternative citrate synthase, and des, encoding a FA desaturase, were upregulated. The sodA gene encoding a manganese superoxide dismutase was upregulated in the presence of Cr(VI), whereas sodB encoding an iron superoxide dismutase was downregulated. Cr(VI) resistance mechanisms in strain AqSCr seem to be orchestrated by the alternative sigma factors fecl, rpoE, and rpoS (all of them upregulated). Membrane lipid analysis of the Cr(IV)-adapted strain showed a lower proportion of unsaturated lipids with respect to the control, which we hypothesized could result from unsaturated lipid peroxidation followed by degradation, together with de novo synthesis mediated by the upregulated FA desaturase-encoding gene, des. This report helps to elucidate both Cr(VI) toxicity targets and global bacterial response to Cr(VI).

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress

Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.

Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications

Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.

Hexavalent chromium reducing bacteria: mechanism of reduction and characteristics

As a common heavy metal, chromium and its compounds are widely used in industrial applications, e.g., leather tanning, electroplating, and in stainless steel, paints and fertilizers. Due to the strong toxicity of Cr(VI), chromium is regarded as a major source of pollution with a serious impact on the environment and biological systems. The disposal of Cr(VI) by biological treatment methods is more favorable than traditional treatment methods because the biological processes are environmentally friendly and cost-efficient. This review describes how bacteria tolerate and reduce Cr(VI) and the effects of some physical and chemical factors on the reduction of Cr(IV). The practical applications for Cr(VI) reduction of bacterial cells are also included in this review.

Transcriptome Response of the Tropical Marine Yeast Yarrowia lipolytica on Exposure to Uranium

In our earlier investigation, we reported the consequences of uranium (U)-induced oxidative stress and cellular defense mechanisms alleviating uranium toxicity in the marine yeast Yarrowia lipolytica NCIM 3589. However, there is lack of information on stress response towards uranium toxicity at molecular level in this organism. To gain an insight on this, transcriptional response of Y. lipolytica after exposure to 50 µM uranium was investigated by RNA sequencing at the global level in this study. The de novo transcriptome analysis (in triplicates) revealed 56 differentially expressed genes with significant up-regulation and down-regulation of 33 and 23 transcripts, respectively, in U-exposed yeast cells as compared to the control, U-unexposed cells. Highly up-regulated genes under U-treated condition were identified to be primarily involved in transport, DNA damage repair and oxidative stress. The major reaction of Y. lipolytica to uranium exposure was the activation of oxidative stress response mechanisms to protect the important biomolecules of the cells. On the other hand, genes involved in cell wall and cell cycle regulation were significantly down-regulated. Overall, the transcriptional profiling by RNA sequencing to stress-inducing concentration of uranium sheds light on the various responses of Y. lipolytica for coping with uranium toxicity, providing a foundation for understanding the molecular interactions between uranium and this marine yeast.

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.

Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation

The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.

Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation

Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb₂S₃) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.

A genomic perspective of metal-resistant bacteria from gold particles: Possible survival mechanisms during gold biogeochemical cycling

A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation is a mechanism for mediating the toxic effect of soluble Au produced during particle dissolution. Genome-wide analysis demonstrated that these isolates also possessed various genes that could provide cellular defence enabling survival under heavy-metal stressed condition by mediating the toxicity of heavy metals through active efflux/reduction. Diverse metal-resistant genes or genes clusters (cop, cus, czc, zntand ars) were detected, which could confer resistance to soluble Au. Comparative genome analysis revealed that the majority of detected heavy-metal resistant genes were similar (i.e. orthologous) to those genes of Cupriavidus metallidurans CH34. The detection of heavy-metal resistance, nutrient cycling and biofilm formation genes (pgaABCD, bsmAandhmpS) may have indirect yet important roles when dealing with soluble Au during particle dissolution. In conclusion, the physiological and genomic results suggest that bacteria living on gold particles would likely use various genes to ensure survival during Au-biogeochemical cycling.

Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil

The effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P < 0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.

Metatranscriptomic analysis of adaptive response of anammox bacteria Candidatus 'Kuenenia stuttgartiensis' to Zn(II) exposure

Zn(II) is frequently detected in biological nitrogen removal systems treating high-strength wastewater (e.g., landfill leachate), yet the cellular defense strategies of anammox bacteria against Zn(II) cytotoxicity is largely unknown. To uncover survival mechanisms under Zn(II) stress, responses of enriched anammox bacteria Candidatus 'Kuenenia stuttgartiensis' under exposure of various levels of Zn (II) were investigated through metatranscriptomic sequencing. Although increasing Zn(II) levels (50, 100 and 150 mg/L) resulted in decreasing anammox activities (86.1 ± 0.8%, 66.1 ± 1.4% and 43.9 ± 1.5% of the control, respectively), the viable cells in anammox sludge remained stable. Candidatus 'K. stuttgartiensis' possesses a complex network of regulatory systems to confer cells with the ability against Zn(II) toxicity, including functions related to substrate degradation, Zn(II) efflux, chelation, DNA repair, protein degradation, protein synthesis and signal transduction processes. Particularly, in order to maintain Zn(II) homeostasis, Candidatus 'K. stuttgartiensis' upregulated genes encoding RND efflux family (czcA, czcB, czcC, kustd1923 and kuste2279) for exporting Zn(II) actively. These heavy metal exporting genes could act as "sentinel genes" to detect the initial stage of Zn(II) inhibition on anammox bacteria, which might be beneficial to develop a diagnostic approach to predict the risk of operational failure when Zn(II) shock occurs.

Over-expression of chickpea glutaredoxin (CaGrx) provides tolerance to heavy metals by reducing metal accumulation and improved physiological and antioxidant defence system

Glutaredoxins (Grxs) are small multifunctional redox proteins. Grxs have glutathione-dependent oxidoreductase activity in the presence of glutathione reductase and NADPH. The role of Grxs is well studied in heavy metal tolerance in prokaryotic and mammalian systems but not in plant genera. In the present study, a chickpea glutaredoxin (CaGrx) gene (LOC101493651) has been investigated against metal stress based on its primary screening in chickpea which revealed higher up-regulation of CaGrx gene under various heavy metals (AsIII-25 μM, AsV-250 μM, Cr(VI)-300 μM, and Cd-500 μM) stress. This CaGrx gene was overexpressed in Arabidopsis thaliana and investigated various biochemical and physiological performances under each metal stress. Transgenic plants showed significant up-regulation of the CaGrx gene during qRT-PCR analysis as well as longer roots, higher seed germination, and survival efficiency during each metal stress. The levels of stress markers, TBARS, H₂O_2, and electrolyte leakage were found to be less in transgenic lines as compared to WT revealed less toxicity in transgenics. The total accumulation of AsIII, AsV, and Cr(VI) were significantly reduced in all transgenic lines except Cd, which was slightly reduced. The physiological parameters such as net photosynthetic rate (P_N), stomatal conductance (g_s), transpiration (E), water use efficiency (WUE), photochemical quenching (qP), and electron transport rate (ETR), were maintained in transgenic lines during metal stress. Various antioxidant enzymes such as glutaredoxin (GRX), glutathione reductase (GR), glutathione peroxidase (GPX), glutathione-S-transferase (GST), ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR), antioxidant molecules (ascorbate, GSH) and stress-responsive amino acids (proline and cysteine) levels were significantly increased in transgenic lines which provide metal tolerance. The outcome of this study strongly indicates that the CaGrx gene participates in the moderation of metal stress in Arabidopsis, which can be utilized in biotechnological interventions to overcome heavy metal stress conditions in different crops.

Coupling enhancement of Chromium(VI) bioreduction in groundwater by phosphorus minerals

Groundwater contaminated by hexavalent chromium (Cr(VI)) has posed severe threat to the environment and public health. Although heterotrophic bioremediation has been known as an efficient approach, little is explored on mineral nutrient source addition such as phosphorus minerals. In this study, the stabilization and sustainability of phosphorus minerals for providing phosphorus has been investigated, and the enhancement of Cr(VI) removal by mixed bacterial consortium coupled with phosphorus minerals was also observed and further verified, with 1.4-3.9 times K values (first-order) increase under different conditions. We demonstrated that the applied of phosphorus minerals facilitated the reduction of Cr(VI) and the removal of Cr(III), promoted the resistance of Cr(VI) and the generation of antioxidase, and engendered the evolution of microbial community structures and functional genes. These findings provide a new insight for enhancement of Cr(VI)-contaminated groundwater in-situ remediation.

Advances on the toxicity of uranium to different organisms

The extensive application of radioactive element uranium (U) and its compounds in the nuclear industry has significantly increased the risk of exposure to the environment. Therefore, research on the safety risks and toxicity mechanisms of U exposure has received increasing attention. This paper reviews the toxic effects of U on different species under different conditions, and summarizes the potential toxicity mechanisms. Under the exposure of U, reactive oxygen species (ROS) produced in cells will damage membrane structure in cells, and inhibit respiratory chain reaction by reducing the production of NADH and ATP. It also induce the expression of apoptosis factors such as Bcl-2, Bid, Bax, and caspase family to cause apoptosis cascade reaction, leading to DNA degradation and cell death. We innovatively list some methods to reduce the toxicity of U because some microorganisms can precipitate uranyl ions through biomineralization or reduction processes. Our work provides a solid foundation for further risk assessment of U.