Isolation and characterization of novel Serratia marcescens (AY927692) for pentachlorophenol degradation from pulp and paper mill waste

A feasible approach for azo-dye (methyl orange) degradation by textile effluent isolate Serratia marcescens ED1 strain for water sustainability: AST identification, degradation optimization and pathway hypothesis

Methyl orange (MO) is a dye commonly used in the textile industry that harms aquatic life, soil and human health due to its potential as an environmental pollutant. The present study describes the dye degradation ability of Serratia marcescens strain ED1 isolated from textile effluent and characterized by 16S rRNA gene sequence analysis. The laccase property of bacterial isolate was confirmed qualitatively. The effects of various factors (pH, temperature, incubation time, and dye concentration) were evaluated using Response Surface Methodology (RSM). The maximum dye (MO) degradation was 81.02 % achieved at 37 °C temperature and 7.0 pH with 200 mg/L dye concentration after 48 h of incubation. The beef extract, ammonium nitrate and fructose supplementation showed better response during bioremediation among the different carbon and nitrogen sources. The degree of pathogenicity was confirmed through the simple plate-based method, and an antibiotic resistance profile was used to check the low-risk rate of antibiotic resistance. However, the fate and extinct of degraded MO products were analysed through UV-Vis spectroscopy, FT-IR, and GC-MS analysis to confirm the biodegradation potential of the bacterial strain ED1 and intermediate metabolites were identified to propose metabolic pathway. The phytotoxicity study on Vigna radiata L. seeds confirmed nontoxic effect of degraded MO metabolites and indicates promising degradation potential of S. marcescens strain ED1 to successfully remediate MO dye ecologically sustainably.

Concurrent anaerobic chromate bio-reduction and pentachlorophenol bio-degradation in a synthetic aquifer

Chromate [Cr(VI)] and pentachlorophenol (PCP) coexist widely in the environment and are highly toxic to public health. However, whether Cr(VI) bio-reduction is accompanied by PCP bio-degradation and how microbial communities can keep long-term stability to mediate these bioprocesses in aquifer remain elusive. Herein, we conducted a 365-day continuous column experiment, during which the concurrent removals of Cr(VI) and PCP were realized under anaerobic condition. This process allowed for complete Cr(VI) bio-reduction and PCP bio-degradation at an efficiency of 92.8 ± 4.2% using ethanol as a co-metabolic substrate. More specifically, Cr(VI) was reduced to insoluble chromium (III) and PCP was efficiently dechlorinated with chloride ion release. Collectively, Acinetobacter and Spirochaeta regulated Cr(VI) bio-reduction heterotrophically, while Pseudomonas mediated not only Cr(VI) bio-reduction but also PCP bio-dechlorination. The bio-dechlorinated products were further mineralized by Azospira and Longilinea. Genes encoding proteins for Cr(VI) bio-reduction (chrA and yieF) and PCP bio-degradation (pceA) were upregulated. Cytochrome c and intracellular nicotinamide adenine dinucleotide were involved in Cr(VI) and PCP detoxification by promoting electron transfer. Taken together, our findings provide a promising bioremediation strategy for concurrent removal of Cr(VI) and PCP in aquifers through bio-stimulation with supplementation of appropriate substrates.

Identification of the hcb Gene Operon Involved in Catalyzing Aerobic Hexachlorobenzene Dechlorination in Nocardioides sp. Strain PD653

Nocardioides sp. strain PD653 was the first identified aerobic bacterium capable of mineralizing hexachlorobenzene (HCB). In this study, strain PD653-B2, which was unexpectedly isolated from a subculture of strain PD653, was found to lack the ability to transform HCB or pentachloronitrobenzene into pentachlorophenol. Comparative genome analysis of the two strains revealed that genetic rearrangement had occurred in strain PD653-B2, with a genomic region present in strain PD653 being deleted. In silico analysis allowed three open reading frames within this region to be identified as candidate genes involved in HCB dechlorination. Assays using recombinant Escherichia coli cells revealed that an operon is responsible for both oxidative HCB dechlorination and pentachloronitrobenzene denitration. The metabolite pentachlorophenol was detected in the cultures produced in the E. coli assays. Significantly less HCB-degrading activity occurred in assays under oxygen-limited conditions ([O₂] < 0.5 mg liter^-1) than under aerobic assays, suggesting that monooxygenase is involved in the reaction. In this operon, hcbA1 was found to encode a monooxygenase involved in HCB dechlorination. This monooxygenase may form a complex with the flavin reductase encoded by hcbA3, increasing the HCB-degrading activity of PD653.IMPORTANCE The organochlorine fungicide HCB is widely distributed in the environment. Bioremediation can effectively remove HCB from contaminated sites, but HCB-degrading microorganisms have been isolated in few studies and the genes involved in HCB degradation have not been identified. In this study, possible genes involved in the initial step of the mineralization of HCB by Nocardioides sp. strain PD653 were identified. The results improve our understanding of the protein families involved in the dechlorination of HCB to give pentachlorophenol.

Community rescue in experimental metacommunities

The conditions that allow biodiversity to recover following severe environmental degradation are poorly understood. We studied community rescue, the recovery of a viable community through the evolutionary rescue of many populations within an evolving community, in metacommunities of soil microbes adapting to a herbicide. The metacommunities occupied a landscape of crossed spatial gradients of the herbicide (Dalapon) and a resource (glucose), whereas their constituent communities were either isolated or connected by dispersal. The spread of adapted communities across the landscape and the persistence of communities when that landscape was degraded were strongly promoted by dispersal, and the capacity to adapt to lethal stress was also related to community size and initial diversity. After abrupt and lethal stress, community rescue was most frequent in communities that had previously experienced sublethal levels of stress and had been connected by dispersal. Community rescue occurred through the evolutionary rescue of both initially common taxa, which remained common, and of initially rare taxa, which grew to dominate the evolved community. Community rescue may allow productivity and biodiversity to recover from severe environmental degradation.

Development of a loop-mediated isothermal amplification method for the rapid detection of the dioxin-degrading bacterium Ochrobactrum anthropi in soil

In this study, loop-mediated isothermal amplification (LAMP) and real-time LAMP assays were developed to detect the dioxin-degrading bacterium Ochrobactrum anthropi strain BD-1 in soil. Four primers were designed to use ITS gene amplification for the strain O. anthropi BD-1. The real-time LAMP assay was found to accomplish the reaction by 1 pg of genomic DNA load when used for nucleic acid amplification. This assay was then applied to detect O. anthropi BD-1 in eight soil samples collected from a dioxin-contaminated site. The results demonstrated that these newly developed LAMP and real-time LAMP assays will not only be useful and efficient tools for detecting the target gene, but also be used as molecular tools for monitoring the growth of dioxin-degrading O. anthropi in the soil. This is the first report to demonstrate the use of LAMP assays to monitor the presence of O. anthropi in dioxin-contaminated soil. The application of this method should improve the biomonitoring of dioxin contamination.

Biosorption of heavy metals by Pseudomonas species isolated from sugar industry

Heavy metal-resistant bacteria can be efficient bioremediators of metals and may provide an alternative or additional method to conventional methods of metal removal. In this study, 10 bacterial isolates were isolated from soil samples of a sugar industry, located at Peshawar, Pakistan. Morphological, physiological, and biochemical characteristics of these isolates were observed. Sequence analysis (16S ribosomal RNA) revealed that isolated strains were closely related to the species belonging to the genera Pseudomonas, Arthrobacter, Exiguobacterium, Citrobacter, and Enterobacter Bacterial isolates were resistant with a minimum inhibitory concentration (500-900 ppm) to lead ion (Pb(2+)), (500-600 ppm) nickel ion (Ni(2+)), (500-800 ppm) copper ion (Cu(2+)), and (600-800 ppm) chromium ion (Cr(3+)) in solid media. Furthermore, biosorption of metals proved considerable removal of heavy metals by isolated metal-resistant strains. Pseudomonas sp. reduced 37% (Pb(2+)), 32% (Ni(2+)), 29% (Cu(2+)), and 32% (Cr(3+)) and was thus found to be most effective, whereas Enterobacter sp. reduced 19% (Pb(2+)), 7% (Ni(2+)), 14% (Cu(2+)), and 21% (Cr(3+)) and was found to be least effective. While average reduction of Pb(2+), Ni(2+), Cu(2+), and Cr(3+) by Citrobacter sp. was found to be 24%, 18%, 23%, and 27%, respectively, among recognized species. This study revealed that Pseudomonas sp. may provide a new microbial community that can be used for enhanced remediation of contaminated environment.

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Pentachlorophenol degradation by Janibacter sp., a new actinobacterium isolated from saline sediment of arid land

Many pentachlorophenol- (PCP-) contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, and high salt concentrations. PCP-degrading microorganisms, adapted to grow and prosper in these environments, play an important role in the biological treatment of polluted extreme habitats. A PCP-degrading bacterium was isolated and characterized from arid and saline soil in southern Tunisia and was enriched in mineral salts medium supplemented with PCP as source of carbon and energy. Based on 16S rRNA coding gene sequence analysis, the strain FAS23 was identified as Janibacter sp. As revealed by high performance liquid chromatography (HPLC) analysis, FAS23 strain was found to be efficient for PCP removal in the presence of 1% of glucose. The conditions of growth and PCP removal by FAS23 strain were found to be optimal in neutral pH and at a temperature of 30 °C. Moreover, this strain was found to be halotolerant at a range of 1-10% of NaCl and able to degrade PCP at a concentration up to 300 mg/L, while the addition of nonionic surfactant (Tween 80) enhanced the PCP removal capacity.

Pentachlorophenol remediation by Enterobacter sp. SG1 isolated from industrial dump site

Chlorophenols contamination is serious concern to the environment due toxicity to all forms of life. Among all the chlorophenols, pentachlorophenol (PCP) is more detrimental to the environment. Pentachlorophenol used as pesticide, herbicide, antifungal agent and wood preservative which causes environmental pollution. In the present research a PCP degrading bacterium was isolated and characterized from industrial dump site. This isolate used PCP as its sole source of carbon and energy and was capable of degrading this compound, as indicated by stoichiometric release of chloride, ring cleavage activity and biomass formation. Based on morphological, biochemical and 16S rRNA gene sequence analysis this strain was identified as Enterobacter sp. SG1. Gas Chromatography (GC) analysis revealed that this strain was able to degrade PCP up to a concentration of 2 mM. This study showed that the removal efficiency of PCP by SG1 was found to be very effective and can be used in degradation of PCP contaminated site or waste in the environment.

Enhanced removal of a pesticides mixture by single cultures and consortia of free and immobilized Streptomyces strains

Pesticides are normally used to control specific pests and to increase the productivity in crops; as a result, soils are contaminated with mixtures of pesticides. In this work, the ability of Streptomyces strains (either as pure or mixed cultures) to remove pentachlorophenol and chlorpyrifos was studied. The antagonism among the strains and their tolerance to the toxic mixture was evaluated. Results revealed that the strains did not have any antagonistic effects and showed tolerance against the pesticides mixture. In fact, the growth of mixed cultures was significantly higher than in pure cultures. Moreover, a pure culture (Streptomyces sp. A5) and a quadruple culture had the highest pentachlorophenol removal percentages (10.6% and 10.1%, resp.), while Streptomyces sp. M7 presented the best chlorpyrifos removal (99.2%). Mixed culture of all Streptomyces spp. when assayed either as free or immobilized cells showed chlorpyrifos removal percentages of 40.17% and 71.05%, respectively, and for pentachlorophenol 5.24% and 14.72%, respectively, suggesting better removal of both pesticides by using immobilized cells. These results reveal that environments contaminated with mixtures of xenobiotics could be successfully cleaned up by using either free or immobilized cultures of Streptomyces, through in situ or ex situ remediation techniques.

Simultaneous removal of AOX and COD from real recycled paper wastewater using GAC-SBBR

A lab-scale granular activated carbon sequencing batch biofilm reactor (GAC-SBBR), a combined adsorption and biological process, was developed to treat real wastewater from a recycled paper mill. In this study, one-consortia of mixed culture (4000-5000 mg/L) originating from recycled paper mill activated sludge from Kajang, Malaysia was acclimatized. The GAC-SBBR was fed with real wastewater taken from the same recycled paper mill, which had a high concentration of chemical oxygen demand (COD) and adsorbable organic halides (AOX). The operational duration of the GAC-SBBR was adjusted from 48 h to 24, 12 and finally 8 h to evaluate the effect of the hydraulic retention time (HRT) on the simultaneous removal of COD and AOX. The COD and AOX removals were in the range of 53-92% and 26-99%, respectively. From this study, it was observed that the longest HRT (48 h) yielded a high removal of COD and AOX, at 92% and 99%, respectively.

Pentachlorophenol dechlorination and simultaneous Cr6+ reduction by Pseudomonas putida SKG-1 MTCC (10510): characterization of PCP dechlorination products, bacterial structure, and functional groups

It is the first report in which a novel psychrotrophic Pseudomonas putida SKG-1 strain was evaluated for simultaneous bioremediation of pentachlorophenol and Cr(6+) under various cultural and nutritional conditions. Pentachlorophenol (PCP) dechlorination products, bacterial structure, and functional groups were characterized by gas chromatography and mass spectrometry (GC-MS), scanning electron microscope and energy dispersive X-ray spectroscopy (SEM-EDS), and Fourier-transform infrared (FTIR) techniques. The strain was extremely tolerant to excessively higher individual concentration of PCP (1,400 mg l(-1)) and Cr(6+) (4,300 mg l(-1)). Increasing concentration of PCP and Cr(6+) exerted inhibitory effect on bacterial growth and toxicants' removal. The strain exhibited growth, and concomitantly remediated both the pollutants simultaneously over a broad pH (7.0-9.0) and temperature (28-32 °C) range; maximum growth, PCP dechlorination (87.5%), and Cr(6+) removal (80.0%) occurred at optimum pH 8.0 and 30 °C (from initial PCP 100 mg l(-1) and Cr(6+) 500 mg l(-1)) under shaking (150 rpm) within 72 h incubation. Optimization of agitation (125 rpm) and aeration (0.4 vvm) in bioreactor further enhanced PCP dechlorination by ~10% and Cr(6+) removal by 2%. A direct correlation existed between growth and bioremediation of both the toxicants. Among other heavy metals, mercury exerted maximum and cobalt minimum inhibitory effect on PCP dechlorination and Cr(6+) removal. Chromate reductase activity was mainly associated with the supernatant and cytosolic fraction of bacterial cells. GC-MS analysis revealed the formation of tetrachloro-p-hydroquinone, 2,4,6-trichlorophenol, and 2,6-dichlorophenol as PCP dechlorination products. FTIR spectrometry indicated likely involvement of carbonyl and amide groups in Cr(3+) adsorption, and SEM-EDS showed the presence of chromium on P. putida surface. Thus, our promising isolate can be ecofriendly employed for biotreatment of various industrial wastes contaminated with high PCP and Cr(6+) concentrations.

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.

Isolation and Growth Characteristics of Chromium(VI) and Pentachlorophenol Tolerant Bacterial Isolate from Treated Tannery Effluent for its Possible Use in Simultaneous Bioremediation

The bacterial strains resistant to pentachlorophenol (PCP) and hexavalent chromium [Cr(VI)] were isolated from treated tannery effluent of a common effluent treatment plant. Most of the physico-chemical parameters analyzed were above permissible limits. Thirty-eight and four bacterial isolates, respectively were found resistant to >50 μg/ml concentration of [Cr(VI)] and the same level of PCP. Out of the above 42 isolates, only one was found simultaneously tolerant to higher levels of both PCP (500 μg/ml) and Cr(VI) (200 μg/ml), and hence was selected for further studies. To the best of our knowledge, this is the first report in which a native bacterial isolate simultaneously tolerant to such a high concentrations of Cr(VI) and PCP has been reported. The culture growth was best at 0.4% (w/v) glucose as an additional carbon source and 0.2% (w/v) ammonium chloride as a nitrogen source. The growth results with cow urine as a nitrogen source were comparable with the best nitrogen source ammonium chloride. The isolate exhibited resistance to multiple heavy metals (Pb, As, Hg, Zn, Co & Ni) and to antibiotics nalidixic acid and polymixin-B. The efficacy of bacterial isolate for growth, PCP degradation (56.5%) and Cr(VI) bioremediation (74.5%) was best at 48 h incubation. The isolate was identified as Bacillus sp. by morphological and biochemical tests. The 16S rDNA sequence analysis revealed 98% homology with Bacillus cereus. However, further molecular analysis is underway to ascertain its likelyhood of a novel species.

Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of populus deltoides

Several naphthalene and anthracene degrading bacteria were isolated from rhizosphere of Populus deltoides, which were growing in non-contaminated soil. Among these, four isolates, i.e. Kurthia sp., Micrococcus varians, Deinococcus radiodurans and Bacillus circulans utilized chrysene, benzene, toluene and xylene, in addition to anthracene and naphthalene. Kurthia sp and B. circulans showed positive chemotactic response for naphthalene and anthracene. The mean growth rate constant (K) of isolates were found to increase with successive increase in substrate concentration (0.5 to 1.0 mg/50ml). B. circulans SBA12 and Kurthia SBA4 degraded 87.5% and 86.6% of anthracene while, Kurthia sp. SBA4, B. circulans SBA12, and M. varians SBA8 degraded 85.3 %, 95.8 % and 86.8 % of naphthalene respectively after 6 days of incubation as determined by HPLC analysis.

Pentachlorophenol degradation by Pseudomonas stutzeri CL7 in the secondary sludge of pulp and paper mill

A pentachlorophenol (PCP) mineralizing bacterium was isolated from the secondary sludge of pulp and paper mill and identified as Pseudomonas stutzeri strain CL7. This isolate used PCP as its sole source of carbon and energy and was capable of degrading this compound as indicated by stoichiometric release of chloride and biomass formation. P. stutzeri (CL7) was able to mineralize a high concentration of PCP (600 mg/L) than any previously reported Pseudomonad with PCP as sole carbon source. As the concentration of PCP increased from 50 to 600 mg/L, the reduction in the cell growth was observed and the PCP degradation was more than 90% in all studied concentrations. This isolate was able to remove 66.8% of PCP from the secondary sludge of pulp and paper mill when supplemented with 100 mg/L of PCP and grown for two weeks. This study showed that the removal efficiency of PCP by CL7 was found to be very effective and can be used in PCP remediation of pulp paper mill waste in the environment.