Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1

Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

A comprehensive review on chromium (Cr) contamination and Cr(VI)-resistant extremophiles in diverse extreme environments

Chromium (Cr) compounds are usually toxins and exist abundantly in two different forms, Cr(VI) and Cr(III), in nature. Their contamination in any environment is a major problem. Many extreme environments including cold climate, warm climate, acidic environment, basic/alkaline environment, hypersaline environment, radiation, drought, high pressure, and anaerobic conditions have accumulated elevated Cr contamination. These harsh physicochemical conditions associated with Cr(VI) contamination damage biological systems in various ways. However, several unique microorganisms belonging to phylogenetically distant taxa (bacteria, fungi, and microalgae) owing to different and very distinct physiological characteristics can withstand extremities of Cr(VI) in different physicochemical environments. These challenging situations offer great potential and extended proficiencies in extremophiles for environmental and biotechnological applications. On these issues, the present review draws attention to Cr(VI) contamination from diverse extreme environmental regions. The study gives a detailed account on the ecology and biogeography of Cr(VI)-resistant microorganisms in inhospitable environments, and their use for detoxifying Cr(VI) and other applications. The study also focuses on physiological, multi-omics, and genetic engineering approaches of Cr(VI)-resistant extremophiles.

Hexavalent chromium removal by a resistant strain Bacillus cereus ZY-2009

Bioreduction of Cr(VI) to Cr(III) by reducing microbes has attracted increasing concern. Here, Cr(VI) removal capacity of a Cr(VI)-resistant bacterium isolated from activated sludge was investigated. Based on its physio-biochemical attributes and 16S rDNA sequence analysis, the strain was identified as Bacillus cereus ZY-2009. It grew normally in the media containing 10-100 mg/L Cr(VI), indicating its high resistance to Cr(VI). Under the optimal conditions of pH 7.0, inoculation amount 10%, and temperature 30°C, Cr(VI) was effectively removed, with a removal rate of ∼80%. Co-existing Fe³⁺ and Cu²⁺ greatly increased Cr(VI) removal, but Cd²⁺ showed significant inhibition. Cr(VI) was removed mainly via enzyme-mediated bioreduction but not biosorption. Cr(VI) was reduced by different cell fractions (i.e. extracellular secretions, cytoplasm, and cell envelope), implying that Cr(VI) can be reduced both extracellularly and intracellularly. This strain can be used in the bioremediation of Cr(VI)-containing wastewater, with Fe³⁺ and Cu²⁺ as stimulators.

Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent

AIMS

Hexavalent chromium Cr(VI), a toxic heavy metal, is a serious pollutant of tannery effluent, and its accumulation in soil and water causes severe environmental concerns of increasing public health issues. The present study focus on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Pseudomonas putida and transferred to E. coli DH5α for further studies.

METHODS AND RESULTS

The bacterial cultures were kept under controlled conditions for 72 h to observe the growth rates and bacterial resistance to chromium. When strains wild type and transformant E. coli DH5α were grown in chromium supplemented media revealed significant growth, but strains cured type Pseudomonas putida and E. coli DH5α were minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5α and wild Pseudomonas putida was 42.52 ± 1.48% and 44.46 ± 0.55%, respectively. The culture supernatant of the wild Pseudomonas putida and transformant E. coli DH5α showed an increased reduction of Cr(VI) compared to cell extract supernatant and cell debris due to the extracellular activity of chromium reductase has been responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Pseudomonas putida and transformant E. coli DH5α.

CONCLUSIONS

Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.

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.

Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors

Methane (CH₄) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH₄ cycle that is controlled by the balance between anaerobic production via methanogenesis and CH₄ removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH₄ oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH₄ in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH₄ oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including Fe^III, Mn^IV, As^V, Cr^VI, Se^VI, Sb^V, V^V, and Br^V. In addition, humic substances as well as biochar and perchlorate (ClO₄^-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH₄ and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.

Isolation and characterization of a highly effective bacterium Bacillus cereus b-525k for hexavalent chromium detoxification

The chromate resistant Gram-positive Bacillus cereus strain b-525k was isolated from tannery effluents, demonstrating optimal propagation at 37 °C and pH 8. The minimum inhibitory concentration (MIC) test showed that B. cereus b-525k can tolerate up to 32 mM Cr⁶⁺, and also exhibit the ability to resist other toxic metal ions including Pb²⁺ (23 mM), As³⁺ (21 mM), Zn²⁺ (17 mM), Cd²⁺ (5 mM), Cu²⁺ (2 mM), and Ni²⁺ (3 mM) with the resistance order as Cr ⁶⁺ > Pb²⁺ > As³⁺ >Zn²⁺ >Cd²⁺ >Ni²⁺ >Cu²⁺. B. cereus b-525k showed maximum biosorption efficiency (q) of 51 mM Cr⁶⁺/g after 6 days. Chromate stress elicited pronounced production of antioxidant enzymes such as catalase (CAT) 191%, glutathione transferase (GST) 192%, superoxide dismutase (SOD) 161%, peroxidase (POX) 199%, and ascorbate peroxidase (APOX) (154%). Within B. cereus b-525k, the influence of Cr⁶⁺ stress (2 mM) did stimulate rise in levels of GSH (907%) and non-protein thiols (541%) was measured as compared to the control (without any Cr⁶⁺ stress) which markedly nullifies Cr⁶⁺ generated oxidative stress. The pilot scale experiments utilizing original tannery effluent showed that B. cereus b-525k could remove 99% Cr⁶⁺ in 6 days, thus, it could be a potential candidate to reclaim the chromate contaminated sites.

Recent Progress and Prospects in Catalytic Water Treatment

Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.

Exploring the Cr(VI) removal mechanism of Sporosarcina saromensis M52 from a genomic perspective

Serious hexavalent chromium [Cr(VI)] pollution has continuously threatened ecological security and public health. Microorganism-assisted remediation technology has strong potential in the treatment of environmental Cr(VI) pollution due to its advantages of high efficiency, low cost, and low secondary pollution. Sporosarcina saromensis M52, a strain with strong Cr(VI) removal ability, isolated from coastal intertidal zone was used in this study. Scanning electron microscopy coupled with energy dispersive X-ray analysis indicated M52 was relatively stable under Cr(VI) stress and trace amount of Cr deposited on the cell surface. X-ray photoelectron spectroscopy and X-ray diffraction analyses exhibited M52 could reduce Cr(VI) into Cr(III). Fourier transform infrared spectroscopy showed the bacterial surface was mainly consisted of polysaccharides, phosphate groups, carboxyl groups, amide II (NH/CN) groups, alkyl groups, and hydroxyl groups, while functional groups involving in Cr(VI) bio-reduction were not detected. According to these characterization analyses, the removal of Cr(VI) was primarily depended on bio-reduction, instead of bio-adsorption by M52. Genome analyses further indicated the probable mechanisms of bio-reduction, including the active efflux of Cr(VI) by chromate transporter ChrA, enzymatic redox reactions mediated by reductases, DNA-repaired proteases ability to minimize the ROS damage, and the formation of specific cell components to minimize the biofilm injuries caused by Cr(VI). These studies provided a theoretical basis which was useful for Cr(VI) remediation, especially in terms of increasing its effectiveness. THE MAIN FINDING OF THE WORK: M52 realized the bioremediation of Cr(VI) majorly through bio-reduction, including Cr(VI) efflux, chromate reduction, DNA repair, and the formation of specific cell components, instead of bio-adsorption.

Natural attenuation mechanism of hexavalent chromium in a wetland: Zoning characteristics of abiotic and biotic effects

Natural wetland has great retention effect on Cr(VI) migration due to its abiotic and biotic reduction abilities, however, the zoning characteristics of dominating reduction mechanism along Cr(VI) pollution plume in wetland is still unclear. In this study, a Cr(VI) contaminated natural wetland was explored to investigate the distributions of Cr and Fe in groundwater and sediment, and their relationship with microorganisms according to metagenomics, aiming to reveal the natural attenuation mechanism of Cr(VI) from the perspective of zoning characteristics of abiotic and biotic effects. The wetland was divided into contaminated zone, transition zone and uncontaminated zone according to the contamination states of groundwater and sediment. At the upstream of contaminated zone, Cr(VI) concentration in groundwater was as high as 26.7 mg L^-1, which has significant inhibition effect on microbial growth, and thus chemical reduction of Cr(VI) by natural organic matters (NOMs) dominated in this area, leading to the increasing of H/C and O/C ratios of NOMs because of the oxidation of aromatic moieties. At the downstream of contaminated zone, Cr(VI) concentration in groundwater decreased to less than 4.46 mg L^-1 resulting from dilution and attenuation, but the microbial community was altered substantially, chromate resistant bacteria with ChrA, ChrR, NemA and AzoR genes were enriched, such as Sphingomonas, Mesorhizobium and Comamonadaceae, and thus the direct microbial reduction of Cr(VI) dominated in this area. While at the transition zone, which is located at the front edge of the pollution plume, Cr(VI) could only reached in this area intermittently, and the microbial community remained similar to that of the uncontaminated zone, dominated by Chloroflexi and Acidobateria phylum with dissimilatory ferric iron reduction capacity, and thus Cr(VI) was indirectly reduced by Fe²⁺ intermediately in this area.

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress

Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.

Making waves: Microbe-photocatalyst hybrids may provide new opportunities for treating heavy metal polluted wastewater

Heavy metal contamination has received increasing attention as a growing worldwide environmental problem. Traditional remediation methods are mainly based on adsorption, precipitation and oxidation-reduction, which reduce the availability or toxicity of heavy metal ions. Microbe-photocatalyst hybrids (MPH), which behave as a semi-artificial photosynthetic system, integrate microbial cells with artificial photocatalysts for solar-to-chemical conversion. A few very recent studies indicate that MPH can be applied to treat organic contamination in water. Here, we propose a novel idea that MPH may also have great potential for solving heavy metal pollution. Heavy metals in wastewater could possibly be utilized to synthesize photocatalysts for MPH by microbial mineralization. Photo-induced electrons generated by photocatalysts in MPH can be transferred into microbial cells to promote intracellular enzymatic reductions, which allows heavy metal ions such as Cr⁶⁺ and Se⁴⁺ to be reduced and detoxified. Moreover, heavy metal ions like As³⁺ and Sb³⁺ can be used as sacrificial electron donors to maintain the continuous operation of the MPH, whereby these metal ions are simultaneously oxidized and detoxified. The excellent potential of MPH in the treatment of heavy metal-polluted wastewater is explained and a solution based on MPH is put forward as well as verified experimentally in this work. This solution can realize electron transfer between different metal ions to simultaneously remediate multiple heavy metal ions in wastewater. This finding may bring new hope for treating multiple heavy metal polluted wastewater in the future.

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.

Simultaneous removal of chromate and arsenite by the immobilized Enterobacter bacterium in combination with chemical reagents

Simultaneous chromate [Cr(VI)] reduction and arsenite [As(III)] oxidation is a promising pretreatment process for Cr and As removal. Here, a facultative anaerobic bacterium, Enterobacter sp. Z1, presented capacities of simultaneous Cr(VI) reduction and As(III) oxidation during anoxic cultivation in a wild range of temperature (20-45 °C) and pH (Cerkez et al., 2015; Chen et al., 2015; China Environmental Prote, 1996; Fan et al., 2008, 2019) conditions. Strikingly, strain Z1 could simultaneously contribute up to 92.8% of the reduction of Cr(VI) and 45.8% of the oxidation of As(III) in wastewater. The cells of strain Z1 were embedded with sodium alginate to produce biobeads, and the biobeads exhibited stable ratio of Cr(VI) reduction (91.8%) and As(III) oxidation (29.6%) even in the 5 continuous cycles of wastewater treatment. Moreover, in a process pretreated with the Z1 biobeads followed a precipitation with Ca(OH)₂ and FeCl₃, the removal efficiencies in wastewater were 98.9% and 98.3% for total Cr and As, respectively, which were 44.1% and 9.8% higher than those of using Ca(OH)₂ and FeCl₃, only. The residual amounts of Cr and As met the national standard levels of wastewater discharge. Proteomics analysis showed that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductase (CysH, CysI, CysJ, NemA and HemF) were induced by Cr(VI) and As(III). Moreover, the addition of cysteine to the medium also significantly improved bacterial Cr(VI) reduction rate. Our results provide a novel microbial pretreatment approach for enhancing remediation of Cr(VI) and As(III) pollution in wastewater, and reveal the evident that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductases are associated with the redox conversion of Cr(VI) and As(III).

Chromium metabolism characteristics of coexpression of ChrA and ChrT gene

OBJECTIVE

Serratia sp. S2 is a wild strain with chromium resistance and reduction ability. Chromium(VI) metabolic-protein-coding gene ChrA and ChrT were cloned from Serratia sp. S2, and ligated with prokaryotic expression vectors pET-28a (+) and transformed into E. coli BL21 to construct ChrA, ChrT and ChrAT engineered bacteria. By studying the characteristics of Cr(VI) metabolism in engineered bacteria, the function and mechanism of the sole expression and coexpression of ChrA and ChrT genes were studied.

METHODS

Using Serratia sp. S2 genome as template, ChrA and ChrT genes were amplified by PCR, and prokaryotic expression vectors was ligated to form the recombinant plasmid pET-28a (+)-ChrA, pET-28a (+)-ChrT and pET-28a (+)-ChrAT, and transformed into E. coli BL21 to construct ChrA, ChrT, ChrAT engineered bacteria. The growth curve, tolerance, and reduction of Cr(VI), the distribution of intracellular and extracellular Cr, activity of chromium reductase and intracellular oxidative stress in engineered bacteria were measured to explore the metabolic characteristics of Cr(VI) in ChrA, ChrT, ChrAT engineered bacteria.

RESULTS

ChrA, ChrT and ChrAT engineered bacteria were successfully constructed by gene recombination technology. The tolerance to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrA > ChrT > Control (P < 0.05), and the reduction ability to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrT > ChrA (P < 0.05). The chromium distribution experiments confirmed that Cr(VI) and Cr(III) were the main valence states. Effect of electron donors on chromium reductase activity was NADPH > NADH > non-NAD(P)H (P < 0.05). The activity of chromium reductase increased significantly with NAD(P)H (P < 0.05). The Glutathione and NPSH (Non-protein Sulfhydryl) levels of ChrA, ChrAT engineered bacteria increased significantly (P < 0.05) under the condition of Cr(VI), but there was no significant difference in the indexes of ChrT engineered bacteria (P > 0.05).

CONCLUSION

ChrAT engineered bacteria possesses resistance and reduction abilities of Cr(VI). ChrA protein endows the strain with the ability to resist Cr(VI). ChrT protein reduces Cr(VI) to Cr(III) by using NAD(P)H as electronic donor. The reduction process promotes the production of GSH, GSSG and NPSH to maintain the intracellular reduction state, which further improves the Cr(VI) tolerance and reduction ability of ChrAT engineered bacteria.

Bacilli-Mediated Degradation of Xenobiotic Compounds and Heavy Metals

Xenobiotic compounds are man-made compounds and widely used in dyes, drugs, pesticides, herbicides, insecticides, explosives, and other industrial chemicals. These compounds have been released into our soil and water due to anthropogenic activities and improper waste disposal practices and cause serious damage to aquatic and terrestrial ecosystems due to their toxic nature. The United States Environmental Protection Agency (USEPA) has listed several toxic substances as priority pollutants. Bacterial remediation is identified as an emerging technique to remove these substances from the environment. Many bacterial genera are actively involved in the degradation of toxic substances. Among the bacterial genera, the members of the genus Bacillus have a great potential to degrade or transform various toxic substances. Many Bacilli have been isolated and characterized by their ability to degrade or transform a wide range of compounds including both naturally occurring substances and xenobiotic compounds. This review describes the biodegradation potentials of Bacilli toward various toxic substances, including 4-chloro-2-nitrophenol, insecticides, pesticides, herbicides, explosives, drugs, polycyclic aromatic compounds, heavy metals, azo dyes, and aromatic acids. Besides, the advanced technologies used for bioremediation of environmental pollutants using Bacilli are also briefly described. This review will increase our understanding of Bacilli-mediated degradation of xenobiotic compounds and heavy metals.

The mechanism of nitrate-Cr(VI) reduction mediated by microbial under different initial pHs

To date, comparatively little research is known about the role of pH conditions in bioremediation of Cr(VI) contaminated aquifers. This study explored microbial Cr(VI) reduction and denitrification under different initial pHs. The underlying mechanism was also investigated. When testing 50 mg/L-N nitrate and 10 mg/L Cr(VI), complete contaminants removal was observed at initial pH 10.0 and 11.0, and only 10 %-30 % of removal achieved under other conditions, which might be ascribe to the significant up-regulation of functional genes narG (8.31 and 10.46 folds) and azoR (24.90 and 15.96 folds) at initial pH 10.0 and 11.0. Metagenomic sequencing showed that alkali tolerant bacteria played major roles in the NO₃^--Cr(VI) reduction (i.e. Pannonibacter increased by 13.08 % and 25.24 % at initial pH 10.0 and 11.0), and metabolic pathways of Degradation and Energy were found of increased abundant. Furthermore, a significative study suggested that potential interspecies cooperation existed at initial pH 11.0 to facilitating the simultaneous removal of contaminants, and Pannonibacter indicus might be an important participant in the degradation of contaminants. The results of this study will fully understand the metabolic patterns of bacteria under alkaline conditions, expand the range of available functional bacteria, and enhance the practical aspects of co-contaminants remediation.

The metagenomic landscape of xenobiotics biodegradation in mangrove sediments

Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.

A Bacillus strain TCL isolated from Jharia coalmine with remarkable stress responses, chromium reduction capability and bioremediation potential

Microbial reduction of Cr(VI) to Cr(III) can mitigate environmental chromium toxicity. A chromium, cadmium and nickel tolerating strain TCL with 97% 16S rRNA gene sequence homology to Bacillus cereus was isolated from a derelict open-cast, Tasra Coalmine Lake of Jharia, India. It could tolerate up to Cr₂₀₀₀ [2,000 mg L^-1 Cr(VI)] and completely reduce Cr₂₀₀ within 16 h under heterotrophic condition. TCL grown in ≥ Cr₅₀₀ exhibited multifarious stress responses particularly in its prolonged lag-phase, like cell aggregation, up to two-fold elongation, increased exopolysaccharide production, and stress enzyme activities. These were relieved by increasing inoculum size or nutrient content. Chromium reduction was constitutive, with maximum activities detected in loosely-bound exopolysaccharides and membrane fractions, followed by cytoplasm and spent media. Cr(VI) was efficiently reduced to Cr(III) and >90% was released in spent media. Cells also expressed Cr-induced active efflux pumps. Growing cells or its crude enzyme extracts could efficiently reduce Cr(VI) in diverse temperatures (15-45 °C), pH (5-9); and in presence of other metals (Cd, Cu, Mo, Ni, Pb), oxyanions (SO₄^-2, NO₂^-), and metabolic inhibitors (phenol, NaN₃, EDTA). Growth and reduction were also detected in nutrient-limited minimal salt media, and contaminated leather industry effluent thereby making TCL a potential candidate for 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.

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.

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.

Identification of the main mechanisms involved in the tolerance and bioremediation of Cr(VI) by Bacillus sp. SFC 500-1E

Chromium pollution is a problem that affects different areas worldwide and, therefore, must be solved. Bioremediation is a promising alternative to treat environmental contamination, but finding bacterial strains able to tolerate and remove different contaminants is a major challenge, since most co-polluted sites contain mixtures of organic and inorganic substances. In the present work, Bacillus sp. SFC 500-1E, isolated from the bacterial consortium SFC 500-1 native to tannery sediments, showed tolerance to various concentrations of different phenolic compounds and heavy metals, such as Cr(VI). This strain was able to efficiently remove Cr(VI), even in the presence of phenol. The detection of the chrA gene suggested that Cr(VI) extrusion could be a mechanism that allowed this strain to tolerate the heavy metal. However, reduction through cytosolic NADH-dependent chromate reductases may be the main mechanism involved in the remediation. The information provided in this study about the mechanisms through which Bacillus sp. SFC 500-1E removes Cr(VI) should be taken into account for the future application of this strain as a possible candidate to remediate contaminated environments.

Phosphate solubilization and chromium (VI) remediation potential of Klebsiella sp. strain CPSB4 isolated from the chromium contaminated agricultural soil

In this study, an effort was made to identify an efficient phosphate solubilizing bacterial strain from chromium contaminated agricultural soils. Based on the formation of a solubilized halo around the colonies on Pikovskaya's agar amended with chromium (VI), 10 strains were initially screened out. Out of 10, strain CPSB4, which showed significantly high solubilization zone at different chromium concentrations, was selected for further study. The strain CPSB4 showed significant plant growth promotion traits with chromium (VI) stress under in-vitro conditions in broth. The plant growth promotion activities of the strain decreased regularly, but were not completely lost with the increase in concentration of chromium up to 200 mg L^-1. On subjected to FT-IR analysis, the presence of the functional group, indicating the organic acid aiding in phosphate solubilization was identified. At an optimal temperature of 30 ^°C and pH 7.0, the strain showed around 93% chromium (VI) reduction under in-vitro conditions in broth study. In soil condition, the maximum chromium (VI) reduction obtained was 95% under in-vitro conditions. The strain CPSB4 was identified as Klebsiella sp. on the basis of morphological, biochemical and 16S rRNA gene sequencing. This study shows that the diverse role of the bacterial strain CPSB4 would be useful in the chromium contaminated soil as a good bioremediation and plant growth promoting agent as well.

A minireplicon of plasmid pBMB26 represents a new typical replicon in the megaplasmids of Bacillus cereus group

A new minireplicon (rep26 minireplicon) from pBMB26, the 188 kb indigenous plasmid related to spore-crystal association (SCA) phenotype in Bacillus thuringiensis strain YBT-020, was characterized. A 12 kb EcoRI fragment, which encoded 10 putative open reading frames (ORFs), was capable of supporting replication when cloned in a replication probe vector. Deletion and frame shift mutation analysis showed that a 4.1 kb region encompassing two putative ORFs (orf21 and orf22) was essential for the plasmid replication in B. thuringiensis. Gene orf21 encoding a 49.8 kDa protein (named Rep26) with a helix-turn-helix motif showed no homology with known replication proteins and gene orf22 encoding a protein of 82.6 kDa showed homology to bacterial PcrA helicase. The replication origin of rep26 minireplicon was proved to be located in the coding region of orf21. Plasmid stability experiments indicated that the recombinant plasmid containing rep26 minireplicon has excellent segregational stability. BLASTP analysis revealed that amino acid sequences of ORF21 and ORF22 were well conserved among Bacillus cereus group strains. The rep26 minireplicon was widely distributed and could be defined as a new typical replicon in the megaplasmids of B. cereus group.

Acetate biostimulation as an effective treatment for cleaning up alkaline soil highly contaminated with Cr(VI)

Stimulation of microbial reduction of Cr(VI) to the less toxic and less soluble Cr(III) through electron donor addition has been regarded as a promising approach for the remediation of chromium-contaminated soil and groundwater sites. However, each site presents different challenges; local physicochemical characteristics and indigenous microbial communities influence the effectiveness of the biostimulation processes. Here, we show microcosm assays stimulation of microbial reduction of Cr(VI) in highly alkaline and saline soil samples from a long-term contaminated site in Guanajuato, Mexico. Acetate was effective promoting anaerobic microbial reduction of 15 mM of Cr(VI) in 25 days accompanied by an increase in pH from 9 to 10. Our analyses showed the presence of Halomonas, Herbaspirillum, Nesterenkonia/Arthrobacter, and Bacillus species in the soil sample collected. Moreover, from biostimulated soil samples, it was possible to isolate Halomonas spp. strains able to grow at 32 mM of Cr(VI). Additionally, we found that polluted groundwater has bacterial species different to those found in soil samples with the ability to resist and reduce chromate using acetate and yeast extract as electron donors.

An approach to study ultrastructural changes and adaptive strategies displayed by Acinetobacter guillouiae SFC 500-1A under simultaneous Cr(VI) and phenol treatment

Acinetobacter guillouiae SFC 500-1A, a native bacterial strain isolated from tannery sediments, is able to simultaneously remove high concentrations of Cr(VI) and phenol. In this complementary study, high-resolution microscopy techniques, such as atomic force microscopy (AFM) and transmission electron microscopy (TEM), were used to improve our understanding of some bacterial adaptive mechanisms that enhance their ability to survive. AFM contributed in gaining insight into changes in bacterial size and morphology. It allowed the unambiguous identification of pollutant-induced cellular disturbances and the visualization of bacterial cells with depth sensitivity. TEM analysis revealed that Cr(VI) produced changes mainly at the intracellular level, whereas phenol produced alterations at the membrane level. This strain tended to form more extensive biofilms after phenol treatment, which was consistent with microscopy images and the production of exopolysaccharides (EPSs). In addition, other exopolymeric substances (DNA, proteins) significantly increased under Cr(VI) and phenol treatment. These exopolymers are important for biofilm formation playing a key role in bacterial aggregate stability, being especially useful for bioremediation of environmental pollutants. This study yields the first direct evidences of a range of different changes in A. guillouiae SFC 500-1A which seems to be adaptive strategies to survive in stressful conditions.

Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a Freshwater Wetland

Deinococcus indicus strain DR1, a red-pigmented, arsenic- and radiation-resistant bacterium, was isolated from a water sample of the Dadri wetland, Uttar Pradesh, India. Here, we report a draft genome sequence of this strain, which may provide useful information regarding the genes and pathways involved in heavy-metal bioremediation.

Nitrate effects on chromate reduction in a methane-based biofilm

The effects of nitrate (NO₃^-) on chromate (Cr(VI)) reduction in a membrane biofilm reactor (MBfR) were studied when CH₄ was the sole electron donor supplied with a non-limiting delivery capacity. A high surface loading of NO₃^- gave significant and irreversible inhibition of Cr(VI) reduction. At a surface loading of 500 mg Cr/m²-d, the Cr(VI)-removal percentage was 100% when NO₃^- was absent (Stage 1), but was dramatically lowered to < 25% with introduction of 280 mg N m^-2-d NO₃^- (Stage 2). After ∼50 days operation in Stage 2, the Cr(VI) reduction recovered to only ∼70% in Stage 3, when NO₃^- was removed from the influent; thus, NO₃^- had a significant long-term inhibition effect on Cr(VI) reduction. Weighted PCoA and UniFrac analyses proved that the introduction of NO₃^- had a strong impact on the microbial community in the biofilms, and the changes possibly were linked to the irreversible inhibition of Cr(VI) reduction. For example, Meiothermus, the main genus involved in Cr(VI) reduction at first, declined with introduction of NO₃^-. The denitrifier Chitinophagaceae was enriched after the addition of NO₃^-, while Pelomonas became important when nitrate was removed, suggesting its potential role as a Cr(VI) reducer. Moreover, introducing NO₃^- led to a decrease in the number of genes predicted (by PICRUSt) to be related to chromate reduction, but genes predicted to be related to denitrification, methane oxidation, and fermentation increased.

Production of a microcapsule agent of chromate-reducing Lysinibacillus fusiformis ZC1 and its application in remediation of chromate-spiked soil

Lysinibacillus fusiformis ZC1 is an efficient Cr(VI)-reducing bacterium that can transform the toxic and soluble chromate [Cr(VI)] form to the less toxic and precipitated chromite form [Cr(III)]. As such, this strain might be applicable for bioremediation of Cr(VI) in soil by reducing its bioavailability. The study objective was to prepare a microcapsule agent of strain ZC1 for bioremediation of Cr(VI)-contaminated soil. Using a single-factor orthogonal array design, the optimal fermentation medium was obtained and consisted of 6 g/L corn flour, 12 g/L soybean flour, 8 g/L NH₄Cl and 6 g/L CaCl₂. After enlarged fermentation, the cell and spore densities were 5.9 × 10⁹ and 1.7 × 10⁸ cfu/mL, respectively. The fermentation products were collected and embedded with 1 % gum arabic and 1 % sorbitol as the microcapsule carriers and were subsequently spray-dried. Strain ZC1 exhibited viable cell counts of (3.6 ± 0.44) × 10¹⁰ cfu/g dw after 50-day storage at room temperature. In simulated soil bioremediation experiments, 67 % of Cr(VI) was reduced in 5 days with the inoculation of this microcapsule agent, and the Cr(VI) concentration was below the soil Cr(VI) standard level. The results demonstrated that the microcapsule agent of strain ZC1 is efficient for bioremediation of Cr(VI)-contaminated soil.

Identification of Chromium Resistant Bacteria from Dry Fly Ash Sample of Mejia MTPS Thermal Power Plant, West Bengal, India

Eight chromium resistant bacteria were isolated from a dry fly ash sample of DVC-MTPS thermal power plant located in Bankura, West Bengal, India. These isolates displayed different degrees of chromate reduction under aerobic conditions. According to 16S rDNA gene analysis, five of them were Staphylococcus, two were Bacillus and one was Micrococcus. The minimum inhibitory concentration towards chromium and the ability to reduce hexavalent chromium to trivalent chromium was highest in Staphylococcus haemolyticus strain HMR17. All the strains were resistant to multiple heavy metals (As, Cu, Cd, Co, Zn, Mn, Pb and Fe) and reduced toxic hexavalent chromium to relatively non toxic trivalent chromium even in the presence of these multiple heavy metals. All of them showed resistance to different antibiotics. In a soil microcosm study, S. haemolyticus strain HMR17 completely reduced 4 mM hexavalent chromium within 7 days of incubation.

Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612

We report here the genome sequence of an effective chromium-reducing bacterium, Bacillus cereus strain S612. The size of the draft genome sequence is approximately 5.4 Mb, with a G+C content of 35%, and it is predicted to contain 5,450 protein-coding genes.

Identification of novel members of the bacterial azoreductase family in Pseudomonas aeruginosa

Azoreductases are a family of diverse enzymes found in many pathogenic bacteria as well as distant homologues being present in eukarya. In addition to having azoreductase activity, these enzymes are also suggested to have NAD(P)H quinone oxidoreductase (NQO) activity which leads to a proposed role in plant pathogenesis. Azoreductases have also been suggested to play a role in the mammalian pathogenesis of Pseudomonas aeruginosa. In view of the importance of P. aeruginosa as a pathogen, we therefore characterized recombinant enzymes following expression of a group of putative azoreductase genes from P. aeruginosa expressed in Escherichia coli. The enzymes include members of the arsenic-resistance protein H (ArsH), tryptophan repressor-binding protein A (WrbA), modulator of drug activity B (MdaB) and YieF families. The ArsH, MdaB and YieF family members all show azoreductase and NQO activities. In contrast, WrbA is the first enzyme to show NQO activity but does not reduce any of the 11 azo compounds tested under a wide range of conditions. These studies will allow further investigation of the possible role of these enzymes in the pathogenesis of P. aeruginosa.

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.

Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil

A Cr(VI)-tolerant, Gram-staining-positive, rod-shaped, endospore-forming and facultative anaerobic bacterium, designated as GSS04(T), was isolated from a heavy-metal-contaminated soil. Strain GSS04(T) was Cr(VI)-tolerant with a minimum inhibitory concentration of 600 mg l(-1) and was capable of reducing Cr(VI) under both aerobic and anaerobic conditions. Growth occurred with presence of 0-3 % (w/v) NaCl (optimum 1 %), at pH 5.5-10.0 (optimum pH 7.0) and 15-50 °C (optimum 30-37 °C). The main respiratory quinone was MK-7 and the major fatty acids were anteiso-C15:0 and iso-C15:0. The DNA G+C content was 41.1 mol%. The predominant polar lipid was diphosphatidylglycerol. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relative was Bacillus shackletonii DSM 18868(T) (97.6 %). The DNA-DNA hybridization between GSS04(T) and its closest relatives revealed low relatedness (<70 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS04(T) represents a novel species of the genus Bacillus, for which the name Bacillus dabaoshanensis sp. nov. is proposed. The type strain is GSS04(T) (=CCTCC AB 2013260(T) = KCTC 33191(T)).

Bacterial mechanisms for Cr(VI) resistance and reduction: an overview and recent advances

Chromium pollution is increasing incessantly due to continuing industrialization. Of various oxidation states, Cr(6+) is very toxic due to its carcinogenic and mutagenic nature. It also has deleterious effects on different microorganisms as well as on plants. Many species of bacteria thriving in the Cr(6+)-contaminated environments have evolved novel strategies to cope with Cr(6+) toxicity. Generally, decreased uptake or exclusion of Cr(6+) compounds through the membranes, biosorption, and the upregulation of genes associated with oxidative stress response are some of the resistance mechanisms in bacterial cells to overcome the Cr(6+) stress. In addition, bacterial Cr(6+) reduction into Cr(3+) is also a mechanism of specific significance as it transforms toxic and mobile chromium derivatives into reduced species which are innocuous and immobile. Ecologically, the bacterial trait of reductive immobilization of Cr(6+) derivatives is of great advantage in bioremediation. The present review is an effort to underline the bacterial resistance and reducing mechanisms to Cr(6+) compounds with recent development in order to garner a broad perspective.

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.

Simultaneous decolorization of reactive Orange M2R dye and reduction of chromate by Lysinibacillus sp. KMK-A

Azo dyes constitute the largest and diverse group of dyes, widely used in number of industries that are contributing toward organic and inorganic load of effluent treatment. In the present study, Lysinibacillus sp. KMK-A was able to effectively decolorize Orange M2R dye up to 2000 mg l(-1) (Vmax of 19.6 mg l(-1) h(-1) and Km of 439 mg l(-1)) and reduce Cr(VI) up to 250 mg l(-1) (Vmax of 3.6 mg l(-1) h(-1) and Km 28.3 mg l(-1)). It also has an ability of simultaneous decolorization of Orange M2R dye (200-1000 mg l(-1)) with reduction of Cr(VI) (50-200 mg l(-1)). Significant reduction in total organic carbon content, chemical and biological oxygen demand along with spectroscopic and chromatographic analysis confirmed the biotransformation of Orange M2R. Involvement of enzymes namely azoreductase and chromate reductase was observed during biotransformation. The phyto and geno toxicity studies demonstrated that metabolites of dye degradation were non-toxic. Higher tolerance with simultaneous decolorization and detoxification of azo dyes in presence of Cr(VI) makes Lysinibacillus sp. KMK-A, a potential candidate for eco-friendly remediation of metal contaminated dye effluents.

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.

The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4

The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

In vitro Cr(VI) reduction by cell-free extracts of chromate-reducing bacteria isolated from tannery effluent irrigated soil

Four efficient Cr(VI)-reducing bacterial strains were isolated from rhizospheric soil of plants irrigated with tannery effluent and investigated for in vitro Cr(VI) reduction. Based on 16S rRNA gene sequencing, the isolated strains SUCR44, SUCR140, SUCR186, and SUCR188 were identified as Bacillus sp. (JN674188), Microbacterium sp. (JN674183), Bacillus thuringiensis (JN674184), and Bacillus subtilis (JN674195), respectively. All four isolates could completely reduce Cr(VI) in culture media at 0.2 mM concentration within a period of 24-120 h; SUCR140 completely reduced Cr(VI) within 24 h. Assay with the permeabilized cells (treated with Triton X-100 and Tween 80) and cell-free assay demonstrated that the Cr(VI) reduction activity was mainly associated with the soluble fraction of cells. Considering the major amount of chromium being reduced within 24-48 h, these fractions could have been released extracellularly also during their growth. At the temperature optima of 28 °C and pH 7.0, the specific activity of Cr(VI) reduction was determined to be 0.32, 0.42, 0.34, and 0.28 μmol Cr(VI)min(-1)mg(-1) protein for isolates SUCR44, SUCR140, SUCR186, and SUCR188, respectively. Addition of 0.1 mM NADH enhanced the Cr(VI) reduction in the cell-free extracts of all four strains. The Cr(VI) reduction activity in cell-free extracts of all the isolates was stable in presence of different metal ions tested except Hg(2+). Beside this, urea and thiourea also reduced the activity of chromate reduction to significant levels.

Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

Reutilization of immobilized fungus Rhizopus sp. LG04 to reduce toxic chromate

AIMS

Most of the researches investigating immobilized fungi in chromate [Cr(VI)] bioremediation have used dead cells to adsorb Cr(VI). Therefore, the aim was to identify a Cr(VI)-reducing fungus with the ability of reducing the toxic Cr(VI) into the much less toxic Cr(III) and to apply the immobilized living fungus in continual reduction of Cr(VI).

METHODS AND RESULTS

Cr(VI) reduction occurred using both free fungi and immobilized living Rhizopus sp. LG04. The Cr(VI) bioreduction by the free fungi was achieved mainly by bioreduction coupled with a small amount of biosorption on the cell surfaces. LG04 spores immobilized with 3% polyvinyl alcohol and 3% sodium alginate produced the most stable and efficient biobeads. When the LG04 biobeads were washed and transferred into fresh medium containing 42 mg l(-1) of Cr(VI), the biobeads could be reused to reduce Cr(VI) for more than 30 cycles during an 82-day operation period. Interestingly, as the cycles increased, the time required for complete reduction stabilized at approximately 2·5 days, which was faster than that obtained using the free fungi (4·5 days). The pH value of the solution decreased from 6·60 ± 0·10 to 3·85 ± 0·15 after each reduction cycle, which may be because the metabolic products of the fungus changed the environmental pH or because there was an accumulation of the organo-Cr(III) complex.

CONCLUSIONS

The results indicate that using the immobilized living fungus for the removal of Cr(VI) has the advantages in being stable, long-term treatment, easy to re-use and less biomass leakage.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this study reports the first successful use of immobilized living Rhizopus for the repeated reduction of Cr(VI).

Strategies for chromium bioremediation of tannery effluent

Bioremediation offers the possibility of using living organisms (bacteria, fungi, algae,or plants), but primarily microorganisms, to degrade or remove environmental contaminants, and transform them into nontoxic or less-toxic forms. The major advantages of bioremediation over conventional physicochemical and biological treatment methods include low cost, good efficiency, minimization of chemicals, reduced quantity of secondary sludge, regeneration of cell biomass, and the possibility of recover-ing pollutant metals. Leather industries, which extensively employ chromium compounds in the tanning process, discharge spent-chromium-laden effluent into nearby water bodies. Worldwide, chromium is known to be one of the most common inorganic contaminants of groundwater at pollutant hazardous sites. Hexavalent chromium poses a health risk to all forms of life. Bioremediation of chromium extant in tannery waste involves different strategies that include biosorption, bioaccumulation,bioreduction, and immobilization of biomaterial(s). Biosorption is a nondirected physiochemical interaction that occurs between metal species and the cellular components of biological species. It is metabolism-dependent when living biomass is employed, and metabolism-independent in dead cell biomass. Dead cell biomass is much more effective than living cell biomass at biosorping heavy metals, including chromium. Bioaccumulation is a metabolically active process in living organisms that works through adsorption, intracellular accumulation, and bioprecipitation mechanisms. In bioreduction processes, microorganisms alter the oxidation/reduction state of toxic metals through direct or indirect biological and chemical process(es).Bioreduction of Cr6+ to Cr3+ not only decreases the chromium toxicity to living organisms, but also helps precipitate chromium at a neutral pH for further physical removal,thus offering promise as a bioremediation strategy. However, biosorption, bioaccumulation, and bioreduction methods that rely on free cells for bioremediation suffer from Cr6 toxicity, and cell damage. Therefore, immobilization of microbial cell biomass enhances bioremediation and renders industrial bioremediation processes more economically viable from reduced free-cells toxicity, easier separation of biosorbents from the tannery effluent, ability to achieve multiple biosorption cycles, and desorption (elution) of metal(s) from matrices for reuse. Thus, microbial bioremediation can be a cost competitive strategy and beneficial bioresource for removing many hazardous contaminants from tannery and other industrial wastes.