Assessment of heavy metal tolerance and biosorptive potential of Klebsiella variicola isolated from industrial effluents

Impact of current anthropogenic activities on Blesbokspruit wetland microbiome and functions

Till present, natural wetlands have been continuously subjected to intensive pollution stress in recent years, mainly because of the rapidly growing industrialization and urbanization that are associated with a myriad of anthropogenic activities and land use practices. These man-made sources of pollution change the chemical properties of the natural wetlands, which in turn alter their microbial ecological biodiversity and functions. For the first time, the impact of the current anthropogenic activities and land use practices on the Blesbokspruit wetland chemical status and their consequential effect on the microbial structure and functions were investigated. Sites of high pollution intensity were identified using geographic information systems mapping (GISMapping) and the wetland microbiome and functional profile were studied through the use of high throughput shotgun metagenomics sequencing analysis. The predominant phyla that stemmed along the Blesbokspruit wetland were found to be Proteobacteria which was more dominant in water (93 %) than in the sediments (89 %), followed by firmicutes which was more abundant in sediments (9 %) than in water (6 %), and Bacteroidetes were relatively low in abundance within both the sediments (2 %) and the overlying water (1 %). The genera Klebsiella (70.4 %-28.2 %), Citrobacter (52.0 %-30.6 %), Escherichia (51.0 %-8.4 %), and Lynsinibacillus (9.3 %-1.5 %) were observed in most water and sediment samples. Within the six polluted sites, Site 2 was found to be the most highly polluted site in the Blesbokspruit wetland with very high COD (900 mg/L), TOC (11.60 mg/L), NO3- (39.74 mg/L), NO2- (12.64 mg/L), PO43 (4.14 mg/L), Fl- (143.88 mg/L), Cl- (145.95 mg/L) concentrations recorded in the water and high levels of TOC (0.37 mg/L), TC (6.92 %), TN (1.82 %), TS (0.53 %) in sediments. The microbial community structure and functions were found to be strongly influenced by the high organic content from the intense agricultural activities and sewage spillages and heavy metals from the mining activities nearby.

Genetic response analysis of Beauveria bassiana Z1 under high concentration Cd(II) stress

Cadmium (Cd(II)) has carcinogenic and teratogenic toxicity, which can be accumulated in the human body through the food chain, endangering human health and life. In this study, a highly Cd(II)-tolerant fungus named Beauveria bassiana Z1 was studied, and its Cd(Ⅱ) removal efficiency was 71.2% when the Cd(II) concentration was 10 mM. Through bioanalysis and experimental verification of the transcriptome data, it was found that cadmium entered the cells through calcium ion channels, and then complexed with intracellular glutathione (GSH) and stored in vacuoles or excluded extracellular by ABC transporters. Cytochrome P450 was significantly upregulated in many pathways and actively participated in detoxification related reactions. The addition of cytochrome inhibitor taxifolin reduced the removal efficiency of Cd(II) by 45%. In the analysis, it demonstrated that ACOX1 gene and OPR gene of jasmonic acid (JA) synthesis pathway were significantly up-regulated, and were correlated with bZIP family transcription factors cpc-1_0 and pa p1_0. The results showed that exogenous JA could improve the removal efficiency of Cd(II) by strain Z1.

Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals

Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.

Enhanced exopolysaccharide production by multi metal tolerant Klebsiella variicolaSMHMZ46 isolated from mines area and application in metal bioremediation

The current study aimed to enhance exopolysaccharide production by Klebsiella variicolaSMHMZ46 isolated from the Zawar mines area in Udaipur, Rajasthan, India, by optimizing the medium with OFAT and a central composite design. The trial including sucrose (9.5%), casein hydrolysate (3%), and NaCl (0.5%) yielded the maximum EPS production as indicated by applying the CCD-RSM biostatistical program. The composition of exopolysaccharides produced by Klebsiella variicolaSMHMZ46 culture was characterized. Growth under Pb(II), Cd(II), and Ni(II) metal amended conditions induced EPS production relative to control. TLC was used for identifying the sugar residues of EPS, in addition to determination of both total carbohydrate and protein contents. According to FT-IR analysis, EPS can interact with metal ions via their functional chemical groups, thereby supporting their bioremediation potential. The metal removal efficiency of bacteria and their produced EPS in broth individually spiked with Pb(II), Ni(II), and Cd(II) was 99.18%, 97.60%, and 98.20%, respectively, and powdered EPS from contaminated water was 85.76%, 72.40%, and 71.53%, respectively. According to FEG-SEM observations, the surface morphology of EPS becomes rough, demonstrating sharp bumps after metal binding. A FEG-SEM analysis of the structure of EPS was performed; the surface structure of EPS (with metal) was more rigid than that of control EPS (without metal). The interaction between the EPS system and Pb(II) ions was investigated using FEG-SEM coupled with energy dispersive X-ray spectra, and a strong peak of C, O, and Pb elements was observed, indicating successful Pb adsorption. These findings suggest that EPS from Klebsiella variicolaSMHMZ46 has a good metal adsorbing nature and could be a promising biosorbent for metal bioremediation of contaminated water.

Optimized Green Nanoemulsions to Remove Pharmaceutical Enoxacin from Contaminated Bulk Aqueous Solution

We attempted to develop green nanoemulsions (ENE1-ENE5) using capryol-C90 (C90), lecithin, Tween 80, and N-methyl-2-pyrrolidone (NMP). HSPiP software and experimentally obtained data were used to explore excipients. ENE1-ENE5 nanoemulsions were prepared and evaluated for in vitro characterization parameters. An HSPiP based QSAR (quantitative structure-activity relationship) module established a predictive correlation between the Hansen solubility parameter (HSP) and thermodynamic parameters. A thermodynamic stability study was conducted under stress conditions of temperature (from -21 to 45 °C) and centrifugation. ENE1-ENE5 were investigated for the influence of size, viscosity, composition, and exposure time on emulsification (5-15 min) on %RE (percent removal efficiency). Eventually, the treated water was evaluated for the absence of the drug using electron microscopy and optical emission spectroscopy. HSPiP program predicted excipients and established the relationship between enoxacin (ENO) and excipients in the QSAR module. The stable green nanoemulsions ENE-ENE5 possessed the globular size range of 61-189 nm, polydispersity index (PDI) of 0.1-0.53, viscosity of 87-237 cP, and ζ potential from -22.1 to -30.8 mV. The values of %RE depended upon the composition, globular size, viscosity, and exposure time. ENE5 showed %RE value as 99.5 ± 9.2% at 15 min of exposure time, which may be due to the available maximized adsorption surface. SEM-EDX (scanning electron microscopy-X-ray dispersive energy mode) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) negated the presence of ENO in the treated water. These variables were critical factors for efficient removal of ENO during water treatment process design. Thus, the optimized nanoemulsion can be a promising approach to treat water contaminated with ENO (a potential pharmaceutical antibiotics).

Development of Ni(II) resistant S. cerevisiae and its application: Adsorption study and modeling

The study aims to develop Ni(II) resistant Saccharomyces cerevisiae to decontaminate high Ni(II) concentrations from an aqueous system. Initially, two different microorganisms were taken: Bacillus circulans MTCC 3161, Saccharomyces cerevisiae. For these two strains, the experiments were carried out for successive screening for survival/tolerance, minimum inhibitory concentration (MIC), and biosorption capacity for Ni(II) from an aqueous solution. Ni(II) resistant Saccharomyces cerevisiae AJ208 showed a MIC of 5500 mg/L for Ni(II). Nucleotide sequences of Saccharomyces cerevisiae AJ208 were deposited in the Gene bank. All experiments were conducted to determine the effects of various physical conditions, such as pH, age and volume of inoculum, temperature, and incubation time, the volume of fermentation medium. The characterization of the Saccharomyces cerevisiae AJ208 was carried out using SEM-EDAX, FTIR. The Langmuir isotherm and pseudo-second-order kinetic models are well fitted with the experimental data. The Langmuir maximum adsorption capacity is 170.06 mg/g. The thermodynamic studies showed the mechanism of Ni(II) removal is an endothermic and spontaneous reaction. The experimental data have been analyzed using statistical method (MLR) and Genetic algorithm (GA). This study reports the highest Ni(II) resistant Saccharomyces cerevisiae AJ208 (5000 mg/L) and also the feasibility of Ni(II) removal from 3000 mg/L initial Ni(II) concentration into an aqueous solution, which could be of great interest as a potential reference strain for Ni(II) removal.

Sustainable utilization of unavoidable food waste into nutritional media for the isolation of bacterial culture for the removal of heavy metals

This study aims to reuse food waste (FW) as growth media for bacterial cultures for bioremediation of heavy metal. The best natural medium was selected based on the carbon, nitrogen, and other elements. The batch culture of Comamonas terrae showed growth stability for 16 days in the pig bone medium. C. terrae showed the best growth at pH of 7.4, temperature of 35 °C, and medium concentration of 10 g/L. The C. terrae showed heavy metal (HM) removal efficiencies of Cd (52 %) Cr (63 %) Pb (62 %) and Zn (55 %). In addition, the Fourier transform infrared spectroscopy results revealed the bioadsorption of HM in C. terrae. The study suggests the C. terrae can efficiently remove HM and C. terrae may be used for bioremediation of HM. Therefore, pig bone waste is a cost-effective medium and a good solution for the valorization and reuse of FW in line with the circular economy.

A manganese-oxidizing bacterium-Enterobacter hormaechei strain DS02Eh01: Capabilities of Mn(II) immobilization, plant growth promotion and biofilm formation

While biogenic Mn oxides (BioMnO_x) generated by Mn(II)-oxidizing bacteria (MOB) have attracted increasing attention, a MOB strain isolated from Mn-polluted sediments was identified and assigned as Enterobacter hormaechei DS02Eh01. Its Mn(II) immobilization activity, plant growth-promoting traits, and biofilm formation capability were investigated. The results showed that strain DS02Eh01 was found to be able to tolerate Mn(II) up to 122 mM. The strain immobilized Mn(II) in aquatic media mainly through extracellular adsorption, bio-oxidation and pH-induced precipitation as well as manganese oxidation. DS02Eh01-derived BioMnO_x are negatively charged and have a larger specific surface area (86.70 m²/g) compared to the previously reported BioMnO_x. The strain can immobilize Mn(II) at extreme levels, for instance, when it was exposed to 20 mM Mn(II), about 59% of Mn(II) were found immobilized and 17% of Mn(II) were converted to MnO_x. The SEM and TEM observation revealed that the DS02Eh01-derived BioMnO_x were aggregates doped with granules and microbial pellets. The precipitated Mn(II) and the Mn(III)/Mn(IV) oxides co-existed in BioMnO_x, in which Mn(II) and Mn(IV) were found dominant with Mn(II) accounting for 49.6% and Mn(IV) accounting for 41.3%. DS02Eh01 possesses plant growth-promoting traits and biofilm formation capacity even under Mn(II) exposure. Mn(II) exposure at 5 mM was found to stimulate strain DS02Eh01 to form biofilms, from which, the extracted EPS was mainly composed of aromatic proteins. This study reveals that E. hormaechei strain DS02Eh01 possesses the potential in environmental ecoremediation via coupling processes of macrophytes extraction, biochemical immobilization and biosorption.

Tolerance and Cadmium (Cd) Immobilization by Native Bacteria Isolated in Cocoa Soils with Increased Metal Content

Twelve cadmium native bacteria previously isolated in soils of cocoa farms located in the western Colombian Andes (Santander), and tolerant to 2500 µM CdCl2 (120 mg Cd/L), were chosen in order to test their tolerance and Cd immobilization using liquid culture medium (Nutritive broth) at different concentrations of heavy metals. Furthermore, in the greenhouse experiments, the strains Exiguobacterium sp. (11-4A), Klebsiella variicola sp. (18-4B), and Enterobacter sp. (29-4B) were applied in combined treatments using CCN51 cacao genotype seeds grown in soil with different concentrations of Cd. All bacterial strains’ cell morphologies were deformed in TEM pictures, which also identified six strain interactions with biosorption and four strain capacities for bioaccumulation; FT-IR suggested that the amide, carbonyl, hydroxyl, ethyl, and phosphate groups on the bacteria biomass were the main Cd binding sites. In the pot experiments, the concentration of Cd was distributed throughout the cacao plant, but certain degrees of immobilization of Cd can occur in soil to prevent an increase in this level in roots with the presence of Klebsiella sp.

Bioremediation of quinclorac injury on tobacco by a rhizosphere bacterium

The presence of herbicides residues in soil represents a serious problem for agriculture. Quinclorac is a common herbicide applied in rice field, but its residue can cause abnormal growth in successive crop of tobacco in Southern China. Remediation by microorganisms is considered to be an environmentally friendly method to remove such pollutants injury. The aims of this study were to obtain quinclorac remediation isolates and to investigate the possible mechanism(s) of remediation. Six bacterial isolates were obtained from rhizosphere of rice-tobacco rotation fields, and were found to be capable of degrading quinclorac on a mineral salt medium (MSM), with degradation efficiency ranging from 2.1 to 23.7%. Among these isolates, J5 had the highest degradation efficiency, and was identified as Klebsiella variicola based on phylogenetic analyses and a metabolic profile generating by Biolog GEN III system. Bioremediation of quinclorac injury was confirmed using pot assays with tobacco, in which J5 reversed the detrimental effect of quinclorac on leaf area, leaf number, and plant height. The J5 isolate also seemed to promote plant growth, in terms of tobacco seedling growth and seed germination, which were 2.2 times and 1.6 times higher compared to untreated control, respectively. The mechanisms of plant growth promoting (PGP) traits were found to involve nitrogen-fixing, indole-3-acetic acid (IAA) production, and phosphate solubilization ability. In addition, proteomic analysis and relative quantitative PCR revealed an elevated level of 4-hydroxyphenylacetate 3-monooxygenase (HPMO) in quinclorac-treated J5, suggesting that this enzyme may play an important role in quinclorac remediation. This study showed that the J5 isolate could be exploited to not only assist in soil remediation due to quinclorac residue issues but also promote tobacco growth.

Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology

Elevated concentration of non-essential persistent heavy metals and metalloids in the soil is detrimental to essential soil microbes and plants, resulting in diminished diversity and biomass. Thus, isolation, screening, and whole genomic analysis of potent strains of bacteria from arable lands with inherent capabilities of heavy metal resistance and plant growth promotion hold the key for bio remedial applications. This study is an attempt to do the same. In this study, a potent strain of Pseudomonas aeruginosa was isolated from paddy fields, followed by metabolic profiling using FTIR, metal uptake analysis employing ICP-MS, whole genome sequencing and comparative codon usage analysis. ICP-MS study provided insights into a high degree of Cd uptake during the exponential phase of growth under cumulative metal stress to Cd, Zn and Co, which was further corroborated by the detection of cadA gene along with czcCBA operon in the genome upon performing whole-genome sequencing. This potent strain of Pseudomonas aeruginosa also harboured genes, such as copA, chrA, znuA, mgtE, corA, and others conferring resistance against different heavy metals, such as Cd, Zn, Co, Cu, Cr, etc. A comparative codon usage bias analysis at the genomic and genic level, whereby several heavy metal resistant genes were considered in the backdrop of two housekeeping genes among 40 Pseudomonas spp. indicated the presence of a relatively strong codon usage bias in the studied strain. With this work, an effort was made to explore heavy metal-resistant bacteria (isolated from arable soil) and whole genome sequence analysis to get insight into metal resistance for future bio remedial applications.

Development of siderophore based rhizobacterial consortium for the mitigation of biotic and abiotic environmental stresses in tomatoes: An in vitro and in planta approach

AIM

Tomato associated plant-growth promoting rhizosphere bacteria were screened for effective antagonistic activity against the fungal vascular wilt pathogens; tolerance to heavy metals; and enhancing the bioavailability of iron for tomato plants through in vitro and in vivo approaches.

METHODS AND RESULTS

Among the 121 rhizobacteria screened for siderophores, 25 isolates were observed to be siderophore producers and out of these, seven isolates chelate copper and iron thus exhibiting in vitro antagonism against the virulent strains of Fusarium oxysporum f. sp. lycopersici MTCC10270 (Fol), Fusarium equiseti MFol, and Sarocladium sp. SWL isolated from infected tomatoes. Pseudomonas stutzeri KRP8 was identified to be the most potent strain among the siderophore producers and its siderophores were chemically characterized by mass spectra as metal bound and metal-free forms. Upon bio-inoculation of fortified bacterial consortium (siderozote) into the rhizosphere of vermiculite pot cultured tomatoes supplied with varying concentrations of iron and copper ions, we observed in planta growth improvements, antagonism, enhancement of bioavailability of iron and heavy metal tolerance using Inductively Coupled Plasma-Optical Emission Spectrometry.

CONCLUSION AND SIGNIFICANCE OF THE STUDY

Our rhizobacterial consortium provides an opportunity for soil reclamation through an ecofriendly method for a heavy metal-free agricultural landscape.

Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen

Klebsiella variicola, a member of Klebsiella pneumoniae complex, is found to infect plants, insects, and animals and is considered an emerging pathogen in humans. While antibiotic resistance is often prevalent among K. variicola isolates from humans, this has not been thoroughly investigated in isolates from nonhuman sources. Prior evidence suggests that K. variicola can be transmitted between agricultural products as well as between animals, and the use of antibiotics in agriculture has increased antibiotic resistance in other emerging pathogens. Furthermore, in animals that contain K. variicola as a normal member of the rumen microbiota, the same bacteria can also cause infections, such as clinical mastitis in dairy cows. Here, we describe K. variicola UFMG-H9 and UFMG-H10, both isolated from the urine of healthy Gyr heifers. These two genomes represent the first isolates from the urine of cattle and exhibit greater similarity with strains from the human urinary tract than isolates from bovine fecal or milk samples. Unique to the UFMG-H9 genome is the presence of flagellar genes, the first such observation for K. variicola. Neither of the sampled animals had symptoms associated with K. variicola infection, even though genes associated with virulence and antibiotic resistance were identified in both strains. Both strains were resistant to amoxicillin, erythromycin, and vancomycin, and UFMG-H10 is resistant to fosfomycin. The observed resistances emphasize the concern regarding the emergence of this species as a human pathogen given its circulation in healthy livestock animals. IMPORTANCE Klebsiella variicola is an opportunistic pathogen in humans. It also has been associated with bovine mastitis, which can have significant economic effects. While numerous isolates have been sequenced from human infections, only 12 have been sequenced from cattle (fecal and milk samples) to date. Recently, we discovered the presence of K. variicola in the urine of two healthy heifers, the first identification of K. variicola in the bovine urinary tract and the first confirmed K. variicola isolate encoding for flagella-mediated motility. Here, we present the genome sequences and analysis of these isolates. The bovine urinary genomes are more similar to isolates from the human urinary tract than they are to other isolates from cattle, suggesting niche specialization. The presence of antibiotic resistance genes is concerning, as prior studies have found transmission between animals. These findings are important to understand the circulation of K. variicola in healthy livestock animals.

Cadmium-Tolerant Plant Growth-Promoting Bacteria Curtobacterium oceanosedimentum Improves Growth Attributes and Strengthens Antioxidant System in Chili (Capsicum frutescens)

The remediation of potentially toxic element-polluted soils can be accomplished through the use of microbial and plant-assisted bioremediation. A total of 32 bacteria were isolated from soil samples contaminated with potentially toxic elements. The isolated bacterial strain DG-20 showed high tolerance to cadmium (up to 18 mM) and also showed bioaccumulative Cd removal properties, as demonstrated by atomic absorption spectroscopy studies. By sequencing the 16S rRNA gene, this strain was identified as Curtobacterium oceanosedimentum. Under stress and normal conditions, isolate DG-20 also produced a wide range of plant growth promoting traits, including ammonia production (51–73 µg/mL) and IAA production (116–183 µg/mL), alongside siderophore production and phosphate solubilization. Additionally, pot experiments were conducted to determine whether the strain could promote Chili growth when Cd salts are present. Over the control, bacterial colonization increased root and shoot lengths significantly up to 58% and 60%, respectively. Following inoculation with the Cd-tolerant strain, the plants also increased in both fresh and dry weight. In both the control and inoculated plants, Cd was accumulated more in roots than in shoots, indicating that Chili was phytostabilizing Cd levels. Besides improving the plant attributes, Cd-tolerant bacteria were also found to increase the amount of total chlorophyll, proline, total phenol, and ascorbic acid in the soil when added to the soil. These results suggest that the inoculant provides protection to plants from negative effects. The results of the present study predict that the combined properties of the tested strain in terms of Cd tolerance and plant growth promotion can be exploited for the purpose of the bioremediation of Cd, and for the improvement of Chili cultivation in soils contaminated with Cd.

Fungal-bacterial biofilm mediated heavy metal rhizo-remediation

Heavy metal pollution due to excessive use of chemical fertilizers (CF) causes major damage to the environment. Microbial biofilms, closely associated with the rhizosphere can remediate heavy metal-contaminated soil by reducing plant toxicity. Thus, this study was undertaken to examine the remedial effects of microbial biofilms against contaminated heavy metals. Fungi and bacteria isolated from soil were screened for their tolerance against Cd²⁺, Pb²⁺, and Zn²⁺. Three bacterial and two fungal isolates were selected upon the tolerance index (TI) percentage. Fungal-bacterial biofilms (FBBs) were developed with the most tolerant isolates and were further screened for their bioremediation capabilities against heavy metals. The best biofilm was evaluated for its rhizoremediation capability with different CF combinations using a pot experiment conducted under greenhouse conditions with potatoes. Significantly (P < 0.05), the highest metal removal percentage was observed in Trichoderma harzianum and Bacillus subtilis biofilm under in situ conditions. When compared to the 100% recommended CF, the biofilm with 50% of the recommended CF (50CB) significantly (P < 0.05) reduced soil available Pb²⁺ by 77%, Cd²⁺ by 78% and Zn²⁺ by 62%. In comparison to initial soil, it was 73%, 76%, and 57% lower of Pb²⁺, Cd²⁺, and Zn²⁺, respectively. In addition, 50CB treatment significantly (P < 0.05) reduced the metal penetration into the tuber tissues in comparison with 100 C. Thus, the function of the developed FBB with T. harzianum-B. subtilis can be used as a potential solution to remediate soil polluted with Pb²⁺ Cd²⁺ and Zn²⁺ metal contaminants.

Bacterial adaptive strategies to cope with metal toxicity in the contaminated environment - A review

Heavy metal contamination poses a serious environmental hazard, globally necessitating intricate attention. Heavy metals can cause deleterious health hazards to humans and other living organisms even at low concentrations. Environmental biotechnologists and eco-toxicologists have rigorously assessed a plethora of bioremediation mechanisms that can hamper the toxic outcomes and the molecular basis for rejuvenating the hazardous impacts, optimistically. Environmental impact assessment and restoration of native and positive scenario has compelled biological management in ensuring safety replenishment in polluted realms often hindered by heavy metal toxicity. Copious treatment modalities have been corroborated to mitigate the detrimental effects to remove heavy metals from polluted sites. In particular, Biological-based treatment methods are of great attention in the metal removal sector due to their high efficiency at low metal concentrations, ecofriendly nature, and cost-effectiveness. Due to rapid multiplication and growth rates, bacteria having metal resistance are advocated for metal removal applications. Evolutionary implications of coping with heavy metals toxicity have redressed bacterial adaptive/resistance strategies related to physiological and cross-protective mechanisms. Ample reviews have been reported for the bacterial adaptive strategies to cope with heavy metal toxicity. Nevertheless, a holistic review summarizing the redox reactions that address the cross-reactivity mechanisms between metallothionein synthesis, extracellular polysaccharides production, siderophore production, and efflux systems of metal resistant bacteria are scarce. Molecular dissection of how bacteria adapt themselves to metal toxicity can augment novel and innovative technologies for efficient detoxification, removal, and combat the restorative difficulties for stress alleviations. The present comprehensive compilation addresses the identification of newer methodologies, summarizing the prevailing strategies of adaptive/resistance mechanisms in bacterial bioremediation. Further pitfalls and respective future directions are enumerated in invigorating effective bioremediation technologies including overexpression studies and delivery systems. The analysis will aid in abridging the gap for limitations in heavy metal removal strategies and necessary cross-talk in elucidating the complex cascade of events in better bioremediation protocols.

Optimizing Bioremediation: Elucidating Copper Accumulation Mechanisms of Acinetobacter sp. IrC2 Isolated From an Industrial Waste Treatment Center

Acinetobacter sp. IrC2 is a copper-resistant bacterium isolated from an industrial waste treatment center in Rungkut, Surabaya. Copper-resistant bacteria are known to accumulate copper inside the cells as a mechanism to adapt to a copper-contaminated environment. Periplasmic and membrane proteins CopA and CopB have been known to incorporate copper as a mechanism of copper resistance. In the present study, protein profile changes in Acinetobacter sp. IrC2 following exposure to copper stress were analyzed to elucidate the copper resistance mechanism. Bacteria were grown in a Luria Bertani agar medium with and without CuSO4 supplementation. Intracellular copper ion accumulation was quantified using atomic absorption spectrophotometry. Changes in protein profile were assessed using sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results showed that 6 mM CuSO4 was toxic for Acinetobacter sp. IrC2, and as a response to this copper-stress condition, the lag phase was prolonged to 18 h. It was also found that the bacteria accumulated copper to a level of 508.01 mg/g of cells' dry weight, marked by a change in colony color to green. The protein profile under copper stress was altered as evidenced by the appearance of five specific protein bands with molecular weights of 68.0, 60.5, 38.5, 24.0, and 20.5 kDa, suggesting the presence of CopA, multicopper oxidase (MCO), CopB, universal stress protein (Usp), and superoxide dismutase (SOD) and/or DNA-binding protein from starved cells, respectively. We proposed that the mechanism of bacterial resistance to copper involves CopA and CopB membrane proteins in binding Cu ions in the periplasm and excreting excess Cu ions as well as involving enzymes that play a role in the detoxification process, namely, SOD, MCO, and Usp to avoid cell damage under copper stress.

Heavy metal tolerance of bacterial isolates associated with overburden strata of an opencast coal mine of Assam (India)

Coal overburden strata (OBS) vary in thickness, geochemical composition, and physical properties from stratum to stratum. Here, we enumerated the cultivable bacterial diversity and their distribution in different OBS taken from the opencast mining of Tikok colliery, Assam. The pH of the coal OBS ranged from 2.46 to 7.93, but 73% of the OBS was acidic. The OBS samples were mostly of shale types except for a few that were sandstone, mudstone, and red soil. The bacterial CFUs per gram OBS samples were highly diverse ranging from 52 to 57.4×10⁴. A total of 79 bacterial pure culture isolates belonging to 19 genera, 12 family, and 3 phyla (Actinobacteria, Firmicutes, and Proteobacteria) were recovered in nutrient agar plates. Firmicutes appeared dominant over the others. All the isolates were screened for heavy metal tolerance in broth culture augmented with five different metals (Ni²⁺, Cu²⁺, Cr⁶⁺, As³⁺, and Cd²⁺) separately. The number of isolates that showed tolerance was 95% for Cr⁶⁺, 69.6% for Ni²⁺, 50.6% each for As³⁺ and Cu²⁺, and 7.6% for Cd²⁺. The bacterial isolates with high metal tolerance, i.e., 5 to 12 mM could be promising for bioremediation of Ni²⁺, Cu²⁺, Cr⁶⁺, and As³⁺ from the sites contaminated with these heavy metals.

Physicochemical and molecular characterization of heavy metal-tolerant bacteria isolated from soil of mining sites in Nigeria

Background

Mining for precious metals is detrimental to the composition of soil structure and microbial diversity distribution and is a health risk to human communities around the affected communities. This study was aimed at determining the physical and chemical characteristics and diversity of bacteria in the soil of local mining sites for biosorption of heavy metals.

Results

Results of physical and chemical characteristics showed mean pH values and percentage organic carbon to range from 7.1 to 8.2 and 0.18 to 1.12% respectively with statistical significance between sampling sites (P ≤ 0.05). Similarly, cation exchange capacity, electrical conductivity, moisture, total nitrogen, and carbon/nitrogen ratio (C:N) in the soil ranged between 1.52 to 3.57 cmol/kg, 0.15 to 0.32 ds/m, 0.14 to 0.82%, 0.10 to 0.28%, and 1.7 to 4.8 respectively. The highest heavy metal concentration of 59.01 ppm was recorded in soils obtained from site 3. The enumeration of viable aerobic bacteria recorded the highest mean count of 4.5 × 10⁶ cfu/g observed at site 2 with statistical significance (P ≤ 0.05) between the sampled soils. Alcaligenes faecalis strain UBI, Aeromonas sp. strain UBI, Aeromonas sobria, and Leptothrix ginsengisoli that make up 11.2% of total identified bacteria were able to grow in higher amended concentrations of heavy metals. The evolutionary relationship showed the four heavy metal–tolerant bacteria identified belonged to the phylum Proteobacteria of class Betaproteobacteria in the order Burkholderiales. Heavy metal biosorption by the bacteria showed Alcaligenes faecalis strain UBI having the highest uptake capacity of 73.5% for Cu.

Conclusion

In conclusion, Alcaligenes faecalis strain UBI (MT107249) and Aeromonas sp. strain UBI (MT126242) identified in this study showed promising capability to withstand heavy metals and are good candidates in genetic modification for bioremediation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00251-x.

Exploring the environmental traits and applications of Klebsiella variicola

Klebsiella variicola has been found in various natural niches, alone or in association with other bacteria, and causes diseases in animals and plants with important economic and environmental impacts. K. variicola has the capacity to fix nitrogen in the rhizosphere and soil; produces indole acetic acid, acetoin, and ammonia; and dissolves phosphorus and potassium, which play an important role in plant growth promotion and nutrition. Some members of K. variicola have properties such as halotolerance and alkalotolerance, conferring an evolutionary advantage. In the environmental protection, K. variicola can be used in the wastewater treatment, biodegradation, and bioremediation of polluted soil, either alone or in association with other organisms. In addition, it has the potential to carry out industrial processes in the food and pharmaceutical industries, like the production of maltose and glucose by the catalysis of debranching unmodified oligosaccharides by the pullulanase enzyme. Finally, this bacterium has the ability to transform chemical energy into electrical energy, such as a biocatalyst, which could be useful in the near future. These properties show that K. variicola should be considered an eco-friendly bacterium with hopeful technological promise. In this review, we explore the most significant aspects of K. variicola and highlight its potential applications in environmental and biotechnological processes.

Halotolerant and metalotolerant bacteria strains with heavy metals biorestoration possibilities isolated from Uburu Salt Lake, Southeastern, Nigeria

Environmental contaminations by heavy metals are currently an increasing public health concern globally. One key challenge of these toxic metals is the extremely difficulties involved in their detoxification from the environment and effluents because of their non-degradability. An efficient biologic agent with potentials of remediating these toxic metals may ease these ever-increasing problems. We reported toxic metals tolerance and bioremediation potentials of novel bacteria sp. Strains USL2S, USL4W and USL5W isolated from Uburu salt lake, Ebonyi State, Nigeria. The phenotypic characteristics and the 16S rRNA gene analyses revealed that USL2S strain belongs to the genus Klebsiella, whereas USL4W and USL5W strains belong to the genus Pseudomonas. The bacteria isolates grew well in media containing 5–15 % of sodium chloride. The bacteria isolate showed capacity to tolerate 50.0 mM Hg⁺² and Pb⁺², 17.0, 12.50 and 4.0mM Ni⁺², Cd⁺², and Zn⁺² respectively in solid media. Pseudomonas putida A4W Strain also tolerated 16.0 mM Cu⁺², while Klebsiella sp. Strain USL2S, Pseudomonas putida USL5W Strain tolerated 4.0 mM each. AAS analyses showed 85, 95, and 95 % Hg; 97.13, 98.89, and 97.55 % Pb; 73.33, 77.42 and 69.72 Cd; 88.06, 99.54, and 97.91 % Ni; 100, 100 and 83.62% Cu; 42.30, 84.52 and 98.80 % Zn removal from media broth incorporated with the tested metals by Klebsiella sp. USL2S, Pseudomonas sp. Strain USL5W and Pseudomonas sp. USL4W respectively. We therefore recommend these novel moderately halophilic and metal tolerant isolates as possible biologic agents for effective bioremediation of mercury, lead, cadmium, nickel, copper and zinc in contaminated environments and effluents.

Evaluation of the Potential Role of Bacillus altitudinis MT422188 in Nickel Bioremediation from Contaminated Industrial Effluents

The incessant pervasiveness of heavy metals in the environment is one of the precursory factors of pollution. This research study was endeavored upon to investigate the bioremediation potential of a nickel (Ni)-resistant bacterial isolate, identified as Bacillus altitudinis MT422188, whose optimum growth parameters were demonstrated at pH 7, temperature 32 °C, and 1 mM phosphate. Minimal Inhibitory Concentration (MIC) and EC50 for Ni were observed to be 20 and 11.5 mM, respectively, whereas the cross heavy-metal resistance was discerned as Cu2+ (25 mM) > Zn2+ (15 mM) > Cr6+ (10 mM) > Pb2+ (5 mM) > Co2+ (8 mM) > Cd2+ (3 mM) > Hg2+ (0 mM). Ni biosorption studies by live and heat-killed bacterial cells were suggestive of Ni uptake being facilitated by an ATP-independent efflux system. A pilot-scale study displayed the effective removal of Ni (70 mg/L and 85 mg/L) at 4- and 8-day intervals, respectively. Moreover, chemotaxis and motility assays indicated the role of Ni as a chemoattractant for bacterial cells. The presence of Ni reduced the GR (0.001 ± 0.003 Ug−1FW), POX (0.001 ± 0.001 Ug−1FW), and SOD (0.091 ± 0.003 Ug−1FW) activity, whereas Sodium dodecyl sulphate—Polyacrylamide gel electrophoresis (SDS-PAGE) revealed the presence of metallothionein (60 kDa). Kinetic and isotherm studies suggested a pseudo second-order and Freundlich model to be better fitted for our study. The thermodynamic parameters (∆H° = 3.0436 kJ/mol, ∆S° = 0.0224 kJ/mol/K) suggested the process to be endothermic, spontaneous, and favorable in nature. FTIR analysis elucidated the interaction of hydroxyl and carboxyl groups with Ni. Scanning Electron Microscopy (SEM) and Energy Dispersive X-Ray Spectroscopy (EDS) demonstrated changes in the morphological and elemental composition of the bacterial cells, which affirmed their interaction with Ni during biosorption. In summary, our study concludes the efficient role of Bacillus altitudinis MT422188 in removing Ni from polluted industrial effluents.

Toxic element profile of ice cream in Bangladesh: a health risk assessment study

Ice cream is a popular frozen dairy product and a possible source of dietary minerals. However, ice cream may also contain toxic metals, which may cause several health implications. The current study aimed to determine the content of toxic elements in ice cream samples using inductively coupled plasma-optical emission spectrometry (ICP-OES) and to assess the health risks of consumers based on target cancer risk (TCR), target hazard quotient (THQ), and hazardous index (HI). The determined concentration (median, range) of all studied elements had shown a descending order of Al (9.36, 5.37-14.26) > Zn (5.94, 1.95-10.22) > Cu (1.73, 1.02-3.77) > Ni (0.95, 0.67-1.80) > Fe (0.79, 0.10-1.64) > Cr (0.43, 0.28-0.73) > Mn (0.42, 0.11-1.03) > Pb (0.34, 0.09-0.79) > Cd (0.08, 0.04-0.14) mg/kg (fresh weight). The values of THQ and HI (except 16% for children) were lower than the maximum threshold risk limit (TRL = 1.0), indicating no potential non-carcinogenic health effects might occur. Similarly, the TCR of Cr and Pb for both adults and children was within the permissible limit of 10^-4-10^-6, which suggested that the consumer would not experience potential lifetime carcinogenic health risks. However, the overall analyses revealed that the consumption of ice cream is almost safe for people, but the combined impact of all metals (HI) in some samples is a matter of health concern. Henceforth, regular monitoring of toxic metals in ice creams should be done to assure food safety and hygiene.

Decolorization and discovery of metabolic pathway for the degradation of Mordant Black 11 dye by Klebsiella sp. MB398

Extensive utilization of the synthetic dyes in various industries is leading to water and soil contamination and ultimately impacting the humans. A research study was conducted for investigating the biodecolorization and biotransformation of Mordant Black 11 dye. For this purpose, potential of biofilm forming bacteria Klebsiella pneumoniae MB398 isolated from effluent outlets of Tops Food Industry, Hattar, Pakistan, was assessed to decolorize and transform Mordant Black 11 dye. Bacterial strain MB398 exhibited the capability of growing optimally at acidic pH (pH 6.0). Klebsiella pneumoniae MB398 efficiently decolorized Mordant Black 11 dye (64.55%) in aerobic environment at pH 6.0 and 37 °C over 24 h, which further increased to 75.35% over a period of 72 h of incubation. Strain MB398 also exhibited the capability of decolorizing Mordant Black 11 dye in the presence of cadmium (63.71%), chromium (61.78%), and copper (61.50%), respectively. UV-VIS spectrophotometric analysis, FTIR, and HPLC spectra were also indicative of biotransformation of dye molecules by Klebsiella pneumoniae MB398. GC-MS analysis of Mordant Black 11 dye revealed formation of 9 novel and unique metabolites including phenol,2,4-bis(1,1-dimethylethyl); 9-eicosene, (E); ethanol,2,2-(2-propenyloxy); acetic acid, benzene; 1-naphthol; methyl formate; valeraldehyde,2,4-dimethyl; and 7-hexadecene (Z). A possible metabolic pathway depicting the biotransformation of Mordant Black 11 dye by Klebsiella pneumoniae MB398 was projected. Findings of the current research study strongly suggest application of Klebsiella pneumoniae MB398 for developing large scale bioremediation strategies for the abatement of synthetic dyes to retain environmental sustainability in bioeconomic way.

Exemplifying an archetypal thorium-EPS complexation by novel thoriotolerant Providencia thoriotolerans AM3

It is the acquisition of unique traits that adds to the enigma of microbial capabilities to carry out extraordinary processes. One such ecosystem is the soil exposed to radionuclides, in the vicinity of atomic power stations. With the aim to study thorium (Th) tolerance in the indigenous bacteria of such soil, the bacteria were isolated and screened for maximum thorium tolerance. Out of all, only one strain AM3, found to tolerate extraordinary levels of Th (1500 mg L⁻¹), was identified to be belonging to genus Providencia and showed maximum genetic similarity with the type strain P. vermicola OP1T. This is the first report suggesting any bacteria to tolerate such high Th and we propose to term such microbes as ‘thoriotolerant’. The medium composition for cultivating AM3 was optimized using response surface methodology (RSM) which also led to an improvement in its Th-tolerance capabilities by 23%. AM3 was found to be a good producer of EPS and hence one component study was also employed for its optimization. Moreover, the EPS produced by the strain showed interaction with Th, which was deduced by Fourier Transform Infrared (FTIR) spectroscopy.

Cd-tolerant SY-2 strain of Stenotrophomonas maltophilia: a potential PGPR, isolated from the Nanjing mining area in China

Microbial and plant assisted bioremediation is an emerging way for the remediation of soils polluted with heavy metals. To screen the cadmium tolerant bacteria, soil samples were collected from Nanjing mining area, China. The average cadmium content of the mine soil reached 45.71 mg/kg, which was indicating serious pollution and potential ecological risk. From the mine soil, six cadmium tolerant plant growth-promoting rhizobacteria (PGPR) were isolated. The isolated bacterial strain "SY-2" showed maximum cadmium tolerance and it was selected for further experimentation. This strain was identified as Stenotrophomonas maltophilia by 16S rRNA gene sequencing (GenBank accession number MG597057). SY-2 was found to tolerate maximum cadmium at 1.0 mM concentration. This strain also exhibited good adsorption capacity (up to 35.7%) of heavy metal at 0.5 mM concentration. The results of this study exhibited organic phosphorus solubilization (37.08 mg/L) and IAA biosynthesis (15.11 mg/L) ability of isolated S. maltophilia. Scanning electron microscopy (SEM) revealed cell shrinkage and the cell wall of S. maltophilia was very rough. Moreover, the energy dispersive X-ray (EDX) analysis endorsed the adsorption of Cd ions on the surface of biomass. FT-IR study described the presence of functional groups and the nature of chemical bonds, before and after cadmium stress. At 0.25 mM cadmium concentration, S. maltophilia treated seeds of Capsicum annuum L. developed 1.46 times longer roots than untreated seeds. The results of this study helped us to conclude that SY-2 strain of S. maltophilia possesses significant metal tolerance and bioremediation potential against cadmium. In the future, this strain can be used as a microbial remediation agent to detoxify heavy metals in contaminated soils.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s13205-020-02524-7s) contains supplementary material, which is available to authorized users.

Detection of Heavy Metal Tolerance among different MLSB Resistance Phenotypes of Methicillin-Resistant S. aureus (MRSA)

Methicillin-resistant Staphylococcus aureus (MRSA) strains are widespread globally. Besides their virulence factors, the co-occurrence of antimicrobial and metal resistance has been reported. This study was designed to evaluate the antibiotic resistance and resistance phenotypes, investigate the occurrence of virulence factors, and detect heavy metal tolerance among MRSA strains. Antibiogram profiling was done as recommended by CLSI instructions. Resistance phenotypes were detected by D test, followed by characterization of enzymatic activities and biofilm formation assay. Antibacterial activity of different heavy metals was tested, and predictable synergistic assay was performed. Among MRSA strains collected, high resistance to ampicillin and amoxicillin/clavulanate (100%) and high susceptibility to clindamycin (70%) were obtained. Resistance phenotypes were detected as S, constitutive MLSB, inducible MLSB, and MS by percentages of 10%, 30%, 30% and 30% respectively. Virulence factors like lipolytic (50%) and hemolytic (70%) activity, and biofilm formation ability (100%) were detected. High resistance towards potassium and magnesium was observed. MTC of 500 ppm was detected for all isolates in case of cobalt and iron. In case of zinc and copper, MTC was detected as 500 ppm except for one isolate which was highly resistant, and 500 ppm for all isolates except for two isolates which were highly sensitive respectively. Magnesium in different concentrations (500 and 2000 ppm) showed synergistic activity with erythromycin and clindamycin. Results reveal high heavy metal tolerance among antibiotic resistant MRSA strains, in addition to the presence of virulence factors. Upcoming studies must be focused on the combination of sub-inhibitory concentration of different heavy metals with the available antibiotics.

Zinc tolerant plant growth promoting bacteria alleviates phytotoxic effects of zinc on maize through zinc immobilization

The increasing heavy metal contamination in agricultural soils has become a serious concern across the globe. The present study envisages developing microbial inoculant approach for agriculture in Zn contaminated soils. Potential zinc tolerant bacteria (ZTB) were isolated from zinc (Zn) contaminated soils of southern Rajasthan, India. Isolates were further screened based on their efficiency towards Zn tolerance and plant growth promoting activities. Four strains viz. ZTB15, ZTB24, ZTB28 and ZTB29 exhibited high degree of tolerance to Zn up to 62.5 mM. The Zn accumulation by these bacterial strains was also evidenced by AAS and SEM-EDS studies. Assessment of various plant growth promotion traits viz., IAA, GA₃, NH₃, HCN, siderophores, ACC deaminase, phytase production and P, K, Si solubilization studies revealed that these ZTB strains may serve as an efficient plant growth promoter under in vitro conditions. Gluconic acid secreted by ZTB strains owing to mineral solubilization was therefore confirmed using high performance liquid chromatography. A pot experiment under Zn stress conditions was performed using maize (Zea mays) variety (FEM-2) as a test crop. Zn toxicity reduced various plant growth parameters; however, inoculation of ZTB strains alleviated the Zn toxicity and enhanced the plant growth parameters. The effects of Zn stress on antioxidant enzyme activities in maize under in vitro conditions were also investigated. An increase in superoxide dismutase, peroxidase, phenylalanine ammonia lyase, catalase and polyphenol oxidase activity was observed on inoculation of ZTB strains. Further, ZIP gene expression studies revealed high expression in the ZIP metal transporter genes which were declined in the ZTB treated maize plantlets. The findings from the present study revealed that ZTB could play an important role in bioremediation in Zn contaminated soils.

Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium-a proteomic approach

Cellular response against different heavy metal stress differs with the metal. Arsenic and chromium are heavy metals and toxic to living systems. The concentration of these metals in seawater is very low. However, due to their solubility in nature, they actively enter cells via various transport mechanisms and cause damage to the cells. Brevibacterium casei #NIOSBA88, a marine-derived, gram-positive isolate was multi-metal tolerant. Proteomic analysis of this isolate in response to arsenic and chromium resulted in the identification of total 2549 proteins, out of which 880 proteins were found to be commonly expressed at 750 mgL^-1 arsenic and 100 mgL^-1 chromium and in absence of both the metals. In contrast, 533, 212, and 270 proteins were found to be unique in the absence of any metal, 750 mgL^-1 of arsenic and 100 mgL^-1 of chromium respectively. Proteins such as antibiotic biosynthesis monooxygenase, ArsR family transcriptional regulator, cytochrome C oxidase subunit II, and thioredoxin reductase were exclusively expressed only in response to arsenic and chromium. Other proteins like superoxide dismutase, lipid hydroperoxide reductase, and thioredoxin-disulfide reductase were found to be upregulated in response to both the metals. Most of the proteins involved in the normal cell functioning were found to be downregulated. Major metabolic functions affected include amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism. Peptide mass fingerprinting of Brevibacterium casei #NIOSBA88 exposed to arsenic and chromium respectively revealed the deleterious effect of these metals on the bacterium and its strategy to overcome the stress.

Assessment of cadmium tolerance and biosorptive potential of Bacillus Cereus GCFSD01 isolated from cadmium contaminated soil

Continuous occurrence of heavy metals is a major cause of environmental pollution due to its toxic effects. At minimum concentrations, these metals are highly reactive and can gather in the food chains and food web, causing major dangers to public health concerns. Soil samples were collected from Paharang drain, Faisalabad. Cadmium tolerant bacteria were isolated and evaluated for their MIC against Cd. The isolated bacterial strain GCFSD01 showed MIC value upto 30 mM/L. The bacterial strain with the highest resistance against Cd was selected for further study. Molecular characterization of bacterial isolate GCFSD01 was performed by 16S rRNA which confirmed it as Bacillus cereus. Optimum growth conditions of bacterial strain were also evaluated. Strain GCFSD01 showed optimum growth at pH 7 and 37 °C temperature. Our result revealed that B. cereus strain GCFSD01 reduced 61.3% Cd after 48 hrs. Multiple metal tolerance and Cd reduction by B. cereus indicate its potential for further use for decontamination of polluted soil.

Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia"

Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.

Comparative genome analysis and characterization of a MDR Klebsiella variicola

Klebsiella variicola is an emerging pathogen responsible for causing blood-stream infections, urinary and respiratory tract related diseases in humans. In this report, we describe the genome sequence data and phenotypic characterization of K. variicola strain KV093 isolated from India. Comparative genome sequence analysis revealed the presence of genes linked with virulence, iron acquisition and transport, type 1 and type 3 pili, secretion systems including the capsular gene cluster. The plant-associated genes such as nitrogen fixation, growth and defense mechanisms against oxidative stress were also identified. On performing antibiotic susceptibility testing, growth inhibition, and stress challenge assays it was observed that the drug resistant K. variicola KV093 exhibited cross resistance to various antibiotics, antiseptics, including disinfectants. This report highlights the arsenal of virulence and antibiotic resistance determinants in K. variicola KV093, an effort emphasizing the current pressing need for regular surveillance of K. variicola strains especially in India.

Characterization of novel thorium tolerant Ochrobactrum intermedium AM7 in consort with assessing its EPS-Thorium binding

Currently, radioactive waste is disposed primarily by burial in a deep geological repository. Microorganisms thriving in such contaminated environment show tolerance to radionuclides. In the present study the bacterial flora, from soil sample collected from an area around atomic power station exposed to radionuclides and heavy metals, was cultivated and assessed for thorium (Th) tolerance. Of all the isolates, strain AM7 identified as O. intermedium was selected since it could thrive at high levels of Th (1000 mg L^-1). AM7 was characterized physico-chemically and its culture medium was optimized using central composite design of response surface methodology for assessing its growth properties in presence of Th. The strain also showed exceptional exopolysaccharide (EPS) production and its yield was further analyzed using one factor study to investigate the influence of each medium component. On supplementing the EPS medium with Th, no significant decrease in yield was observed. FTIR spectroscopy revealed the functional groups of EPS involved in EPS-Th binding. To the best of our knowledge, this is the first report showing exceptional Th-tolerance by any bacteria. Such study will help other researchers to strategize an environment-friendly way of radwaste disposal.

Selective metal removal from chromium-containing synthetic effluents using Shewanella xiamenensis biofilm supported on zeolite

A scheme of selective removal of metal ions from chromium-containing synthetic solutions with the following chemical composition, Cr (VI)-Fe (III), Cr (VI)-Fe (III)-Ni (II), Cr (VI)-Fe (III)-Ni (II)-Zn (II), and Cr (VI)-Fe (III)-Ni (II)-Zn (II)-Cu (II)) by Shewanella xiamenensis biofilm immobilized on a zeolite support, was proposed. Three biological processes, biosorption, bioaccumulation, and longtime bioreduction, were applied for metal removal. The process of Zn (II), Ni (II), and Cu (II) showed to be pH dependent. The maximum removal of Ni (II) was achieved during a 1-hour biosorption process at pH 5.0-6.0, of Zn (II) at pH 5.0, and of Cu (II) at pH 3.0. Chromium (VI) and Fe (III) ions were more efficiently removed by bioaccumulation. Chromium (VI) removal in the studied systems varied from 16.4% to 34.8 and of iron from 55.8 to 94.6%. In a long-term bioreduction experiment, it was possible to achieve complete reduction of Cr (VI) to Cr (III) ions by Shewanella xiamenensis in 42 days and by Shewanella xiamenensis biofilm on zeolite in 35 days. Shewanella oneidensis can be effectively used to remove metal ions from chemically complex effluents.

Sustainable microbial cell nanofactory for zinc oxide nanoparticles production by zinc-tolerant probiotic Lactobacillus plantarum strain TA4

BACKGROUND

The use of microorganisms in the biosynthesis of zinc oxide nanoparticles (ZnO NPs) has recently emerged as an alternative to chemical and physical methods due to its low-cost and eco-friendly method. Several lactic acid bacteria (LAB) have developed mechanisms in tolerating Zn²⁺ through prevention against their toxicity and the production of ZnO NPs. The LAB's main resistance mechanism to Zn²⁺ is highly depended on the microorganisms' ability to interact with Zn²⁺ either through biosorption or bioaccumulation processes. Besides the inadequate studies conducted on biosynthesis with the use of zinc-tolerant probiotics, the understanding regarding the mechanism involved in this process is not clear. Therefore, this study determines the features of probiotic LAB strain TA4 related to its resistance to Zn²⁺. It also attempts to illustrate its potential in creating a sustainable microbial cell nanofactory of ZnO NPs.

RESULTS

A zinc-tolerant probiotic strain TA4, which was isolated from local fermented food, was selected based on the principal component analysis (PCA) with the highest score of probiotic attributes. Based on the 16S rRNA gene analysis, this strain was identified as Lactobacillus plantarum strain TA4, indicating its high resistance to Zn²⁺ at a maximum tolerable concentration (MTC) value of 500 mM and its capability of producing ZnO NPs. The UV-visible spectroscopy analysis proved the formations of ZnO NPs through the notable absorption peak at 380 nm. It was also found from the dynamic light scattering (DLS) analysis that the Z-average particle size amounted to 124.2 nm with monodisperse ZnO NPs. Studies on scanning electron microscope (SEM), energy-dispersive X-ray (EDX) spectroscopy, and Fourier-transform infrared spectroscopy (FT-IR) revealed that the main mechanisms in ZnO NPs biosynthesis were facilitated by the Zn²⁺ biosorption ability through the functional groups present on the cell surface of strain TA4.

CONCLUSIONS

The strong ability of zinc-tolerant probiotic of L. plantarum strain TA4 to tolerate high Zn²⁺ concentration and to produce ZnO NPs highlights the unique properties of these bacteria as a natural microbial cell nanofactory for a more sustainable and eco-friendly practice of ZnO NPs biosynthesis.

Molecular epidemiology of Klebsiella variicola obtained from different sources

Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes the molecular epidemiology of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The molecular epidemiology of K. variicola showed a global distribution for some STs was observed, and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST analysis identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum β-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong molecular epidemiological tool that allows following the evolution of this bacterial species obtained from different environments.

Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8-10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

Klebsiella variicola: an emerging pathogen in humans

The Klebsiella pneumoniae complex comprises seven K. pneumoniae-related species, including K. variicola. K. variicola is a versatile bacterium capable of colonizing different hosts such as plants, humans, insects and animals. Currently, K. variicola is gaining recognition as a cause of several human infections; nevertheless, its virulence profile is not fully characterized. The clinical significance of K. variicola infection is hidden by imprecise detection methods that underestimate its real prevalence; however, several methods have been developed to correctly identify this species. Recent studies of carbapenemase-producing and colistin-resistant strains demonstrate a potential reservoir of multidrug-resistant genes. This finding presents an imminent scenario for spreading antimicrobial resistant genes among close relatives and, more concerningly, in clinical and environmental settings. Since K. variicola was identified as a novel bacterial species, different research groups have contributed findings elucidating this pathogen; however, important details about its epidemiology, pathogenesis and ecology are still missing. This review highlights the most significant aspects of K. variicola, discussing its different phenotypes, mechanisms of resistance, and virulence traits, as well as the types of infections associated with this pathogen.