High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes

Molecular insights into biological transformation mechanism of sulfathiazole by Chlorella sorokiniana: Deciphering the uptake, translocation, and biotransformation

As a sustainable approach to wastewater treatment, microalgae have been extensively used to degrade antibiotics. However, the underlying mechanisms involved in the degradation process remain unclear. Therefore, this study investigated the biotransformation mechanism of sulfathiazole (STZ) by Chlorella sorokiniana (C. sorokiniana) at the molecular level. The results show that C. sorokiniana could efficiently degrade STZ, achieving a maximum degradation rate of 94.74 %, mainly through biodegradation routes. Transcriptome analysis has elucidated the potential biological transformation mechanisms driving the degradation of STZ by microalgae, focusing on the uptake, translocation, and biotransformation as key metabolic processes. In particular, STZ induced the up-regulation of genes associated with cell adhesion, membrane protein, and lipopolysaccharide, suggesting their involvement in the uptake of STZ by microalgae. Furthermore, ABC, MATE, and MFS transporters were identified as crucial for the transmembrane transport of STZ by microalgae. A plausible biotransformation pathway for STZ degradation was proposed, identifying hydroxylation, oxidation, ring cleavage, and formylation as the primary transformation processes. The up-regulation of key enzymes such as monooxygenases, dioxygenases, hydrolases, and transferases suggested their pivotal role in the biodegradation of STZ. This research provides valuable insights into the biotransformation mechanisms of STZ by microalgae, thereby laying a theoretical framework to advance the implementation of microalgae in the treatment of antibiotic-contaminated wastewater.

Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant-microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant-microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security.

Biostimulation effect of different amendments on Cr(VI) recovering microbial community

The present study used Cr(VI)-polluted microcosms amended with lactate or yeast extract, and nonamended microcosms as control, to investigate how a native bacterial community varied in response to the treatment and during the pollutant removal. Results suggested that providing electron donors resulted in a proliferation of a few bacterial species, with the consequent decrease in observed species richness and evenness, and was a driving force for the bacterial compositional shift. Lactate promoted, in the first instance, the enrichment of fermentative bacteria belonging to Chromobacteriaceae, including Paludibacterium, and Micrococcaceae as observed after 4 days. When the rate of Cr(VI) removal was maximum in microcosms amended with lactate, the most represented taxa were Pseudarcicella and Azospirillum. Using yeast extract as a carbon source and electron donor led instead to the significant enrichment of Shewanella, followed by Vogesella and Acinetobacter on the 4th day, corresponding to 90% of Cr(VI) removed from the system. After the complete Cr(VI) removal, achieved in 7 days in the presence of yeast extract, α-diversity was notably increased. The amendment-specific turnover of the enriched bacterial taxa resulted in a different kinetic of pollutant removal. In particular, yeast extract promoted the quickest Cr(VI) reduction, while lactate supported a slower, but also considerable, pollutant removal from water. Since it is reasonable to assume that a macroscopic effect, such as the observed Cr(VI) removal, involved the overrepresented taxa, deepening the knowledge of the native bacterial community and its changes were used to hypothesize the possible microbial pathways involved.

Linking groundwater microbiome and functional ecological clusters to geogenic high hexavalent chromium from deep aquifers in a loess plateau

Geogenic high hexavalent chromium [Cr(Ⅵ)] in groundwater is a global environmental problem. However, the groundwater microbiome and its linkage to geogenic high Cr(Ⅵ) from deep aquifers still need to be elucidated. Here, we evaluated geogenic Cr(Ⅵ), groundwater microbiome with featured functional ecological clusters and their interactive responses in groundwater from a deep aquifer in a loess plateau of Northern Shaanxi, China. We found that the compositions and structures of microbial communities in groundwater from the deep aquifer were significantly different between low Cr(Ⅵ) (LCG, < 50 μg/L) and high Cr(Ⅵ) groundwater (HCG, > 50 μg/L), with higher microbial diversity and richness in HCG (p < 0.05). Functional "specialists" related to Cr biotransformation, including Cr(Ⅵ) reducing bacteria (CRB) Rhodococcus, Nocardioides, Novosphingobium, and Acidovorax and Mn-oxidizing bacteria (MnOB) Sphingobium, and Ralstonia were positively correlated to total Cr and Cr(VI) concentrations in groundwater. Moreover, these CRB and MnOB were dominant in high Cr(VI) groundwater and associated by strong interspecific relation in an ecological cluster (p < 0.05), suggesting their indicator roles for high Cr(Ⅵ) and the contribution of MnOB mediated Cr(III) oxidation to Cr(VI) enrichment. RDA and path analysis further revealed that the geogenic Cr(Ⅵ) directly promoted the key Cr-related functional cluster with the groundwater depth, dissolved oxygen, and total dissolved solids as the cofactors indirectly influencing Cr(Ⅵ) and the functional clusters (p < 0.05). Collectively, our results highlight the significant roles of microbial ecological clusters especially functional "specialists" MnOB and CRB in groundwater Cr(Ⅵ) from deep aquifers in the loess plateau and provide a basis for sustainable management of high Cr(Ⅵ) groundwater.

Analysis of the functional gene of degrading BDE-47 by Acinetobacter pittii GB-2 based on transcriptome sequencing

2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) is one of the most widely distributed PBDEs. BDE-47 is also the most abundant in organisms and the most toxic to humans and animals. Herein, we have studied the pathway of BDE-47 degradation and gene involvement in Acinetobacter pittii GB-2. This degradation is dominated by hydroxylation, resulting in hydroxylated products 6-OH-BDE-47, 5-OH-BDE-47 and 2'-OH-BDE-28, and bromophenol products 2,4-DBP and 4-BP. Transcriptome sequencing results showed 359 differentially expressed genes (DEGs) induced by BDE-47, of which 159 were up-regulated and 200 were down-regulated. The up-regulated ones were mainly related to substance transport, degradation and cell stress. From these results, we suggest that 1,2-dioxygenase, phenol hydroxylase and monooxygenase are involved in BDE-47 degradation. The function of AntA gene was identified by constructing a prokaryotic expression vector. Our study contributes to understanding how the metabolism of strain GB-2 changes under BDE-47 stress conditions, and sheds light on the mechanism of BDE-47 degradation.

Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments

Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 10³ ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.

Implantation of Bacillus pseudomycoides Chromate Transporter Increases Chromate Tolerance in Bacillus subtilis

Chromium of anthropogenic origin contaminates the environment worldwide. The toxicity of chromium, a group I human carcinogen, is greatest when it is in a hexavalent oxidation state, Cr(VI). Cr(VI) is actively transported into the cell, triggering oxidative damage intracellularly. Due to the abundance of unspecific intracellular reductants, any microbial species is capable of bio-transformation of toxic Cr(VI) to innocuous Cr(III), however, this process is often lethal. Only some bacterial species are capable of sustaining the vegetative growth in the presence of a high concentration of Cr(VI) and thus operate as self-sustainable bioremediation agents. One of the successful microbial Cr(VI) detoxification strategies is the activation of chromate efflux pumps. This work describes transplantation of the chromate efflux pump from the potentially pathogenic but highly Cr resistant Bacillus pseudomycoides environmental strain into non-pathogenic but only transiently Cr tolerant Bacillus subtilis strain. In our study, we compared the two Bacillus spp. strains harboring evolutionarily diverged chromate efflux proteins. We have found that individual cells of the Cr-resistant B. pseudomycoides environmental strain accumulate less Cr than the cells of B. subtilis strain. Further, we found that survival of the B. subtilis strain during the Cr stress can be increased by the introduction of the chromate transporter from the Cr resistant environmental strain into its genome. Additionally, the expression of B. pseudomycoides chromate transporter ChrA in B. subtilis seems to be activated by the presence of chromate, hinting at versatility of Cr-efflux proteins. This study outlines the future direction for increasing the Cr-tolerance of non-pathogenic species and safe bioremediation using soil bacteria.

Biological removal of hexavalent chromium: evaluation of the metabolic activity of native and Cr(VI)-acclimated activated sludge using a respirometric method

Hexavalent chromium becomes in one of the tops internationally concern environmental issues due to its wide usage in several industrial activities. There are two stable oxidation states of chromium in the environment which differ significantly on its toxicity; Cr(III) has lower solubility, mobility and lesser biological toxicity in comparison with Cr(VI). While Cr(VI) is a well-known carcinogen, Cr(III) is an essential dietary element. For this reason, most technologies focus attention on the reduction of Cr(VI) to Cr(III). On this context, the ability of microorganisms to reduce Cr(VI) to Cr(III) has gained attention. The objectives of the present work were to analyze the effect of Cr(VI) on the activated sludge community in a continuous reactor, and to evaluate the differences on the metabolic activity of native (NAS) and Cr(VI)-acclimated activated sludge (CrAAS) using a respirometric method. Results showed that the activated sludge community had the capability to acclimate to the presence of Cr(VI). On the other hand, the increase of the initial Cr(VI) concentration from 0 to 100 mgCr/L leads to a decrease in the specific exogenous respiration rate (q_Ex ) values, but this reduction was more noticeably in the case of NAS in comparison with CrAAS. The respirometric curves were well described by the proposed mathematical model. It was concluded that the CrAAS tolerated a Cr(VI) concentration about one order of magnitude higher than NAS, which was positively reflected in the respiration rate first-order decay constant (k_d ), the specific maximum exogenous respiration rate (q_Exm ), and the observed oxidation coefficient (Y_O/S ) values.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Mechanisms of Cr(VI) reduction by Bacillus sp. CRB-1, a novel Cr(VI)-reducing bacterium isolated from tannery activated sludge

Cr(VI) reduction by microorganisms has been extensively reported, however, the mechanism of Cr(VI) reduction varies among different microorganisms. In this study, a Cr(VI)-reducing bacterium identified as Bacillus sp. was isolated from tannery activated sludge, strain CRB-1 was able to completely reduce 50 mg/L of Cr(VI) within 24 h under aerobic conditions and exhibited considerable Cr(VI) removal efficiency in the pH range from 7.0 to 9.0, temperature 24-42 °C. Cr(VI) reduction assays with resting cells, permeabilized cells, and subcellular fractions suggested that Cr(VI) reduction mainly occurred in the cytoplasm. According to qRT-PCR analysis, a chrA gene and a nitR2 gene were up-regulated under Cr(VI) stress. Heterologous expression of the chrA gene and the nitR2 gene indicated that ChrA was associated with Cr(VI) resistance, while NitR2 was responsible for Cr(VI) reduction. Furthermore, soluble end products were detected. On the basis of FTIR, it was speculated that the formation of soluble end products may be due to the complexation of EPS with Cr(III). Consequently, the Cr(VI)-reducing ability of strain CRB-1 and its chromate reductases enables CRB-1 a potential candidate for Cr(VI) bioremediation.

Chromate tolerance and removal of bacterial strains isolated from uncontaminated and chromium-polluted environments

Investigation of bacterial chromate tolerance has mostly focused on strains originating from polluted sites. In the present study, we isolated 33 chromate tolerant strains from diverse environments harbouring varying concentrations of chromium (Cr). All of these strains were able to grow on minimal media with at least 2 mM hexavalent chromium (Cr(VI)) and their classification revealed that they belonged to 12 different species and 8 genera, with a majority (n = 20) being affiliated to the Bacillus cereus group. Selected B. cereus group strains were further characterised for their chromate tolerance level and the ability to remove toxic Cr(VI) from solution. A similar level of chromate tolerance was observed in isolates originating from environments harbouring high or low Cr. Reference B. cereus strains exhibited the same Cr(VI) tolerance which indicates that a high chromate tolerance could be an intrinsic group characteristic. Cr(VI) removal varied from 22.9% (strain PCr2a) to 98.5% (strain NCr4). Strains NCr1a and PCr12 exhibited the ability to grow to the greatest extent in Cr(VI) containing media (maximum growth of 65.3% and 64.9% relative to that in the absence of Cr(VI), respectively) accompanied with high chromate removal activity (73.7% and 74.4%, respectively), making them prime candidates for the investigation of chromate tolerance mechanisms in Gram-positive bacteria and Cr(VI) bioremediation applications.

Biodegradation of persistent environmental pollutants by Arthrobacter sp

Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.

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

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

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml⁻¹, chloramphenicol 0–24 μg ml⁻¹, and vancomycin 0–24 μg ml⁻¹). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.

Chromate Resistance Mechanisms in Leucobacter chromiiresistens

Chromate is one of the major anthropogenic contaminants on Earth. Leucobacter chromiiresistens is a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress, L. chromiiresistens forms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of the L. chromiiresistens genome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use of L. chromiiresistens as a new model organism to study microbial chromate resistance.IMPORTANCE Chromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies of L. chromiiresistens to establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.

Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein

Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a V_max of 34.46 µmol/min/mg enzyme and K_m of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.

Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes

Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.

Chromium resistance characteristics of Cr(VI) resistance genes ChrA and ChrB in Serratia sp. S2

OBJECTIVE

To find an efficient chromium (VI) resistance system, with a highly efficient, economical, safe, and environmentally friendly chromium-removing strain, ChrA, ChrB, and ChrAB fragments of the chromium (VI) resistance gene in Serratia sp. S2 were cloned, and their prokaryotic expression vectors were constructed and transformed into E. coli BL21. The anti-chromium (VI) capacity and characteristics of engineered bacteria, role of ChrA and ChrB genes in the anti-chromium (VI) processes, and the mechanism of chromium metabolism, were explored.

METHODS

The PCR technique was used to amplify ChrA, ChrB, and ChrAB genes from the Serratia sp. S2 genome. ChrA, ChrB, and ChrAB genes were connected to the prokaryotic expression vector pET-28a and transferred into E. coli BL21 for prokaryotic expression. Cr-absorption and Cr-efflux ability of the engineered strains were determined. The effects of respiratory inhibitors and oxygenated anions on Cr-efflux of ChrA and ChrB engineered strains were explored.

RESULTS

ChrA, ChrB, and ChrAB engineered strains were constructed successfully; there was no significant difference between the control strain and the ChrB engineered strain for Cr-metabolism (P > 0.05). Cr-absorption and Cr-efflux of ChrA and ChrAB engineered strains were significantly stronger than the control strain (P < 0.05). Oxyanions (sulfate and molybdate) and inhibitors (valinomycin and CN^-) could significantly inhibit the Cr-efflux capacities of ChrA and ChrAB engineered strains (P < 0.05), while NADPH could significantly promote such capacities (P < 0.05).

CONCLUSION

The Cr-transporter, encoded by ChrA gene, confer the ability to pump out intracellular Cr on ChrA and ChrAB engineered strains. The ChrB gene plays a positive regulatory role in ChrA gene regulation. The Cr-metabolism ability of the ChrAB engineered strain is stronger than the ChrA engineered strain. ChrA and ChrAB genes in the Cr-resistance system may involve a variety of mechanisms, such as sulfate ion channel and respiratory chain electron transfer.

Carbon-dependent chromate toxicity mechanism in an environmental Arthrobacter isolate

Arthrobacter spp. are widespread in soil systems and well-known for their Cr(VI) reduction capabilities making them attractive candidates for in situ bioremediation efforts. Cellulose drives carbon flow in soil systems; yet, most laboratory studies evaluate Arthrobacter-Cr(VI) interactions solely with nutrient-rich media or glucose. This study aims to determine how various cellulose degradation products and biostimulation substrates influence Cr(VI) toxicity, reduction, and microbial growth of an environmental Arthrobacter sp. isolate. Laboratory culture-based studies suggest there is a carbon-dependent Cr(VI) toxicity mechanism that affects subsequent Cr(VI) reduction by strain LLW01. Strain LLW01 could only grow in the presence of, and reduce, 50 μM Cr(VI) when glucose or lactate were provided. Compared to lactate, Cr(VI) was at least 30-fold and 10-fold more toxic when ethanol or butyrate was the sole carbon source, respectively. The addition of sulfate mitigated toxicity somewhat, but had no effect on the extent of Cr(VI) reduction. Cell viability studies indicated that a small fraction of cells were viable after 8 days suggesting cell growth and subsequent Cr(VI) reduction may resume. These results suggest when designing bioremediation strategies with Arthrobacter spp. such as strain LLW01, carbon sources such as glucose and lactate should be considered over ethanol and butyrate.

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.

Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination

Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr⁶⁺) to the much less toxic Cr³⁺. In addition, it reduces sulfate (SO₄²⁻) to S²⁻. The S²⁻ could react with Cd²⁺ to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified.

Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants

Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.

Plasmid-Mediated Tolerance Toward Environmental Pollutants

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes.

Characterization and structure prediction of partial length protein sequences of pcoA, pcoR and chrB genes from heavy metal resistant bacteria from the Klip River, South Africa

The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. Copper and chromate resistance determinants were cloned and sequenced. Open reading frames (ORFs) related to the genes CopA and CopR were identified in E. coli KR29, PcoA in Lysinibacillus sp. KR25 and none related to chromate resistance were detected. The 3D-models predicted by I-TASSER disclose that the PcoA proteins consist of β-sheets, which form a part of the cupredoxin domain of the CopA copper resistance family of genes. The model for PcoR_29 revealed the presence of a helix turn helix; this forms part of a DNA binding protein, which is part of a heavy metal transcriptional regulator. The bacterial strains were cured using ethidium bromide. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E. coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element, which was not detected using gel electrophoresis.

The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

BACKGROUND

Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison.

RESULTS

Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia.

CONCLUSIONS

Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.

Global transcriptome analysis of hexavalent chromium stress responses in Staphylococcus aureus LZ-01

Staphylococcus aureus strain LZ-01, isolated from the Lanzhou reaches of the Yellow River, is capable of reducing Cr(VI) to Cr(III) aerobically. We employed transcriptome sequencing analysis to identify genes involved in Cr(VI) stress responses in S. aureus LZ-01. Our results showed that 512 of the 2,370 predicted genes displayed up-regulation (>2-fold), and 49 genes were down-regulated (<50 %) after Cr(VI) exposure. Among up-regulated genes, 128 genes were annotated to encode proteins involved in cellular processes; 68 were categorized to transport and binding proteins; 26 were involved in DNA repair and 32 were associated with regulatory functions. To further elucidate the Cr(VI) resistance and reduction mechanism, we carried out physiological tests and quantitative PCR analysis. Both RNA-seq and qRT-PCR data showed genes encoding a thioredoxin reductase and main subunits of cytochrome c oxidase complex were up-regulated upon Cr(VI) treatment. Either cadmium or NaN3 treatment could inhibit Cr(VI) reduction which indicates that thioredoxin and cytochrome are involved in Cr(VI) reduction strain LZ-01. 29 ABC-type metal/multidrug transporters and efflux pumps were up-regulated, suggesting that they are involved in Cr(VI) resistance by pumping chromium ions out of cells. The up-regulation of 26 DNA repair genes demonstrate that Cr(VI) is toxic to DNA and those DNA protection proteins need to be responded for Cr(VI) stress. Based on these results, the mechanism of strain LZ-01 resists and reduces Cr(VI) is revealed.

Chromate alters root system architecture and activates expression of genes involved in iron homeostasis and signaling in Arabidopsis thaliana

Soil contamination by hexavalent chromium [Cr(VI) or chromate] due to anthropogenic activities has become an increasingly important environmental problem. To date few studies have been performed to elucidate the signaling networks involved on adaptive responses to (CrVI) toxicity in plants. In this work, we report that depending upon its concentration, Cr(VI) alters in different ways the architecture of the root system in Arabidopsis thaliana seedlings. Low concentrations of Cr (20-40 µM) promoted primary root growth, while concentrations higher than 60 µM Cr repressed growth and increased formation of root hairs, lateral root primordia and adventitious roots. We analyzed global gene expression changes in seedlings grown in media supplied with 20 or 140 µM Cr. The level of 731 transcripts was significantly modified in response to Cr treatment with only five genes common to both Cr concentrations. Interestingly, 23 genes related to iron (Fe) acquisition were up-regulated including IRT1, YSL2, FRO5, BHLH100, BHLH101 and BHLH039 and the master controllers of Fe deficiency responses PYE and BTS were specifically activated in pericycle cells. It was also found that increasing concentration of Cr in the plant correlated with a decrease in Fe content, but increased both acidification of the rhizosphere and activity of the ferric chelate reductase. Supply of Fe to Cr-treated Arabidopsis allowed primary root to resume growth and alleviated toxicity symptoms, indicating that Fe nutrition is a major target of Cr stress in plants. Our results show that low Cr levels are beneficial to plants and that toxic Cr concentrations activate a low-Fe rescue system.

Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400

The chromate ion transporter (CHR) superfamily comprises transporters that confer chromate resistance by extruding toxic chromate ions from cytoplasm. Burkholderia xenovorans strain LB400 has been reported to encode six CHR homologues in its multireplicon genome. We found that strain LB400 displays chromate-inducible resistance to chromate. Susceptibility tests of Escherichia coli strains transformed with cloned B. xenovorans chr genes indicated that the six genes confer chromate resistance, although under different growth conditions, and suggested that expression of chr genes is regulated by sulfate. Expression of chr genes was measured by quantitative reverse transcription-PCR (RT-qPCR) from total RNA of B. xenovorans LB400 grown under different concentrations of sulfate and exposed or not to chromate. The chr homologues displayed distinct expression levels, but showed no significant differences in transcription under the various sulfate concentrations tested, indicating that sulfate does not regulate chr gene expression in B. xenovorans. The chrA2 gene, encoded in the megaplasmid, was the only chr gene whose expression was induced by chromate and it was shown to constitute the chromate-responsive chrBACF operon. These data suggest that this determinant is mainly responsible for the B. xenovorans LB400 chromate resistance phenotype.

Molecular mechanisms of Cr(VI) resistance in bacteria and fungi

Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.

Identification and characterization of the transcriptional regulator ChrB in the chromate resistance determinant of Ochrobactrum tritici 5bvl1

Ochrobactrum tritici 5bvl1 is able to resist to high concentrations of chromate through the expression of an inducible chromate-resistant determinant, found in a mobile element (TnOtChr), which carries the genes, chrB, chrA, chrC and chrF. The regulation of chr operon present in TnOtChr, which is controlled by a transcriptional regulator, ChrB, was characterized in the current work. Fusions of chr promoter, or chr promoter and chrB gene, upstream of a gfp reporter gene, identified the most probable promoter sequence within the tnpR-chrB intergenic region. This region contains an AT-rich imperfect inverted repeat sequence, which overlaps a part of the −10 sequence. The results of the in vitro DNA-binding assays with purified ChrB (His- or no-tagged) showed that the protein binds directly to the chr promoter region. In order to identify the ChrB functional domain for sensing chromate stress and for DNA-binding, site-directed mutagenesis of ChrB was performed. Among several single amino acid mutants, three mutants (R180; R187 and H229) prevented chromate induction without any modification to the protein’s stability. Interestingly, two ChrB mutants (R18 and R23) were constitutively active, regardless of chromate stress conditions, indicating that the residues most probably belong to the protein-DNA binding site. As such, the ChrB was classified as a transcriptional regulator that recognizes a specific DNA sequence, regulating the expression of a chromate resistance determinant.

Complete genome sequence of Arthrobacter sp. strain FB24

Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

The pleiotropic effect of WD-40 domain containing proteins on cellular differentiation and production of secondary metabolites in Streptomyces coelicolor

The genome of Streptomyces coelicolor encodes six potential WD-40 genes. Two of them, the wdpB (SCO5953) and the wdpC (SCO4422) genes, were studied to determine their function. Deletion of the wdpB gene resulted in a considerable decrease of aerial hyphae formation, leading to a conditionally bald phenotype, and reduced undecylprodigiosin production. In addition, the aerial hyphae of the ΔwdpB mutant strain were unusually branched and showed the signs of irregular septation and precocious lysis. Disruption of wdpC resulted in the reduction of undecylprodigiosin and delayed actinorhodin production. The ΔwdpC mutant strain showed precocious lysis of hyphae and delayed sporulation without typical curling of aerial hyphae in the early sporulation stage. The whole-genome transcriptome analysis revealed that deletion of wdpB affects the expression of genes involved in aerial hyphae differentiation, sporulation and secondary metabolites production. Deletion of wdpC caused downregulation of several gene clusters encoding secondary metabolites. Both the wdp genes seem to possess transcriptional autoregulatory function. Overexpression and genetic complementation studies confirmed the observed phenotype of both mutants. The results obtained suggest that both genes studied have a pleiotropic effect on physiological and morphological differentiation.

The Neurospora crassa chr-1 gene is up-regulated by chromate and its encoded CHR-1 protein causes chromate sensitivity and chromium accumulation

The ChrA membrane protein belongs to the CHR superfamily of chromate ion transporters, which includes homologues from bacteria, archaea and eukaryotes. Bacterial ChrA homologues confer chromate resistance by exporting chromate ions from the cell's cytoplasm. The Neurospora crassa strain 74-A chr-1 gene encodes a putative CHR-1 protein of 507 amino acid residues, which belongs to the CHR superfamily. RT-PCR assays showed that expression of the chr-1 gene was up-regulated by chromate exposure of N. crassa cultures. Introduction in N. crassa of sense and antisense fragments of the chr-1 gene, as part of a silencing module within the pSilent-1 vector, produced transformants with a phenotype of resistance to chromate and diminished accumulation of chromium, as compared with the control strain containing only the vector. A chromate-resistance phenotype was also observed in N crassa strains deleted in the genomic chr-1 gene, thus confirming that the absence of CHR-1 protein confers chromate resistance to the fungus. The cDNA from N. crassa chr-1 gene (Ncchr-1) was cloned into the pYES2 vector under the control of a GAL promoter and the resulting recombinant plasmid was transferred to the yeast Saccharomyces cerevisiae. Galactose-induced S. cerevisiae transformants expressing Ncchr-1 were more sensitive to chromate and accumulated 2.5 times more chromium than the induced strain containing only the vector. Excess sulfate, a chromate analog, was unable to protect S. cerevisiae chr-1 transformants from chromate toxicity. These data indicate that the N. crassa CHR-1 protein functions as a transporter that takes up chromate; it also appears that this transport occurs in a sulfate-independent fashion. This is the first report assigning a role as a chromate transporter to a nonbacterial CHR protein.

Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a

BACKGROUND

Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-methylquinoline) as sole carbon and energy source. The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain.

RESULTS

The genome of Arthrobacter sp. Rue61a consists of a single circular chromosome of 4,736,495 bp with an average G + C content of 62.32%, the circular 231,551-bp plasmid pARUE232, and the linear 112,992-bp plasmid pARUE113 that was already published. Plasmid pARUE232 is proposed to contribute to the resistance of Arthrobacter sp. Rue61a to arsenate and Pb2+, whereas the linear plasmid confers the ability to convert quinaldine to anthranilate. Remarkably, degradation of anthranilate exclusively proceeds via a CoA-thioester pathway. Apart from quinaldine utilization, strain Rue61a has a limited set of aromatic degradation pathways, enabling the utilization of 4-hydroxy-substituted aromatic carboxylic acids, which are characteristic products of lignin depolymerization, via ortho cleavage of protocatechuate. However, 4-hydroxyphenylacetate degradation likely proceeds via meta cleavage of homoprotocatechuate. The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. It encodes a broad spectrum of enzymes for the uptake and utilization of various sugars and organic nitrogen compounds. A. aurescens TC-1 is the closest sequenced relative of strain Rue61a.

CONCLUSIONS

The genome of Arthrobacter sp. Rue61a reflects the saprophytic lifestyle and nutritional versatility of the organism and a strong adaptive potential to environmental stress. The circular plasmid pARUE232 and the linear plasmid pARUE113 contribute to heavy metal resistance and to the ability to degrade quinaldine, respectively.

Antiparallel membrane topology of paired short-chain chromate transport proteins in Bacillus subtilis

Short-chain monodomain family comprises pairs of membrane proteins of about 200 amino acid residues each that belong to the chromate ion transporter (CHR) superfamily. The short-chain CHR homologous pair Chr3N/Chr3C from Bacillus subtilis strain 168 confers chromate resistance only when both proteins are expressed. Membrane topology of the Chr3N and Chr3C proteins was determined in Escherichia coli by the analysis of translational fusions with reporter enzymes alkaline phosphatase and β-galactosidase. Each short-chain CHR protein was found to consist of five transmembrane segments with antiparallel orientation between them. The C terminus of Chr3N is located in the cytoplasm, whereas the C terminus of Chr3C is located in the periplasm. In silico analyses suggest that this antiparallel arrangement is shared by all protein members of the short-chain CHR3 subfamily and that the two Chr3N/Chr3C proteins might carry out distinct functions for the transport of chromate.

Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile

Background

Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized.

Results

DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively.

Conclusions

This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.

Surface enhanced Raman spectroscopy (SERS) for the discrimination of Arthrobacter strains based on variations in cell surface composition

Surface enhanced Raman spectroscopy (SERS) is a rapid and highly sensitive spectroscopic technique that has the potential to measure chemical changes in bacterial cell surface in response to environmental changes. The objective of this study was to determine whether SERS had sufficient resolution to differentiate closely related bacteria within a genus grown on solid and liquid medium, and a single Arthrobacter strain grown in multiple chromate concentrations. Fourteen closely related Arthrobacter strains, based on their 16S rRNA gene sequences, were used in this study. After performing principal component analysis in conjunction with Linear Discriminant Analysis, we used a novel, adapted cross-validation method, which more faithfully models the classification of spectra. All fourteen strains could be classified with up to 97% accuracy. The hierarchical trees comparing SERS spectra from the liquid and solid media datasets were different. Additionally, hierarchical trees created from the Raman data were different from those obtained using 16S rRNA gene sequences (a phylogenetic measure). A single bacterial strain grown on solid media culture with three different chromate levels also showed significant spectral distinction at discrete points identified by the new Elastic Net regularized regression method demonstrating the ability of SERS to detect environmentally induced changes in cell surface composition. This study demonstrates that SERS is effective in distinguishing between a large number of very closely related Arthrobacter strains and could be a valuable tool for rapid monitoring and characterization of phenotypic variations in a single population in response to environmental conditions.

The ChrA homologue from a sulfur-regulated gene cluster in cyanobacterial plasmid pANL confers chromate resistance

The cyanobacterium Synechococcus elongatus strain PCC 7942 possesses pANL, a plasmid rich in genes related to sulfur metabolism. One of these genes, srpC, encodes the SrpC protein, a homologue of the CHR chromate ion transporter superfamily. The srpC gene was cloned and expressed in Escherichia coli and its role in relation to sulfate and chromate was analyzed. srpC was unable to complement the growth of an E. coli cysA sulfate uptake mutant when sulfate was utilized as a sole sulfur source, suggesting that SrpC is not a sulfate transporter. Expression of srpC in E. coli conferred chromate resistance and caused diminished chromate uptake. These results suggest that the S. elongatus SrpC protein functions as a transporter that extrudes chromate ions from the cell's cytoplasm, and further demonstrate the close relationship between sulfate and chromate metabolism in this organism.

Genome Sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1

Lysinibacillus fusiformis ZC1 isolated from chromium (Cr) contaminated wastewater of a metal electroplating factory displayed high chromate [Cr(VI)] resistance with a minimal inhibitory concentration (MIC) of 60mM in R2A medium. L. fusiformis ZC1 showed resistances to multiple metals (Cu, Ni, Co, Hg, Cd and Ag) and a metalloid (As). This bacterium exhibited an extremely rapid Cr(VI) reduction capability. It almost completely reduced 1mM K(2)CrO(4) in 12h. The Cr(VI) reduction ability of L. fusiformis ZC1 was enhanced by sodium acetate and NADH. By whole genome sequence analysis, strain ZC1 was found to contain large numbers of metal(loid) resistance genes. Specifically, a chrA gene encoding a putative chromate transporter conferring chromate resistance was identified. The chromate resistance was constitutive in both phenotypic and gene expression analyses. Furthermore, we found a yieF gene and several genes encoding reductases that were possibly involved in chromate reduction. Expression of adjacent putative chromate reduction related genes, nitR and yieF, was found to be constitutive. The large numbers of NADH-dependent chromate reductase genes may be responsible for the rapid chromate reduction in order to detoxify Cr(VI) and survive in the harsh wastewater environment.

Chromium genotoxicity: A double-edged sword

Certain forms of hexavalent chromium [Cr(VI)] are known respiratory carcinogens that induce a broad spectrum of DNA damage. Cr(VI)-carcinogenesis may be initiated or promoted through several mechanistic processes including, the intracellular metabolic reduction of Cr(VI) producing chromium species capable of interacting with DNA to yield genotoxic and mutagenic effects, Cr(VI)-induced inflammatory/immunological responses, and alteration of survival signaling pathways. Cr(VI) enters the cell through non-specific anion channels, and is metabolically reduced by agents including ascorbate, glutathione, and cysteine to Cr(V), Cr(IV), and Cr(III). Cr(III) has a weak membrane permeability capacity and is unable to cross the cell membrane, thereby trapping it within the cell where it can bind to DNA and produce genetic damage leading to genomic instability. Structural genetic lesions produced by the intracellular reduction of Cr(VI) include DNA adducts, DNA-strand breaks, DNA-protein crosslinks, oxidized bases, abasic sites, and DNA inter- and intrastrand crosslinks. The damage induced by Cr(VI) can lead to dysfunctional DNA replication and transcription, aberrant cell cycle checkpoints, dysregulated DNA repair mechanisms, microsatelite instability, inflammatory responses, and the disruption of key regulatory gene networks responsible for the balance of cell survival and cell death, which may all play an important role in Cr(VI) carcinogenesis. Several lines of evidence have indicated that neoplastic progression is a result of consecutive genetic/epigenetic changes that provide cellular survival advantages, and ultimately lead to the conversion of normal human cells to malignant cancer cells. This review is based on studies that provide a glimpse into Cr(VI) carcinogenicity via mechanisms including Cr(VI)-induced death-resistance, the involvement of DNA repair mechanisms in survival after chromium exposure, and the activation of survival signaling cascades in response to Cr(VI) genotoxicity.