Co-Metabolic Biodegradation of DBP by Paenibacillus sp. S-3 and H-2

Two di-n-butyl phthalate (DBP)-degrading strains, designated as S-3 and H-2, were isolated from DBP-polluted soil and both identified as Paenibacillus sp. When DBP was provided as the sole carbon source, about 45.5 and 71.7 % of DBP (100 mg/L) were degraded by strain S-3 and H-2, respectively, after incubation for 48 h. However, DBP (100 mg/L) was degraded completely by co-culture of strain S-3 and H-2 after incubation for 60 h. Four phthalic acid (PA) esters could be utilized by co-metabolism in the study and the degradation rates followed the order of dimethyl phthalate > diethyl phthalate > DBP > dioctyl phthalate. The metabolic pathway of DBP was elucidated based on the results of metabolites identification and enzyme assays. For strain S-3, DBP was degraded into butyl hydrogen phthalate which was degraded to PA by carboxyesterase further. But PA could be not hydrolyzed further because strain S-3 lacked 3,4-phthalate dioxygenase. Different with S-3, strain H-2 could hydrolyze PA into 3,4-dihydroxy-PA by 3,4-phthalate dioxygenase. Then 3,4-dihydroxy-PA was converted to protocatechuate and benzoic acid. Finally, the aromatic ring was cleavage and mineralized to CO₂ and H₂O. Above all, co-metabolism could increase the activity of 3,4-phthalate dioxygenase and accelerated the degradation of DBP. This study highlights an important potential use of co-metabolic biodegradation for the in situ bioremediation of DBP and its metabolites-contaminated environment.     

Biodegradation of tributyl phosphate using Klebsiella pneumoniae sp. S3

Tributyl phosphate (TBP) has enormous applications in the field of extraction, fuel reprocessing, as defoamers and/or plasticizers. Excessive usage of this organophosphorus compound, poses an environmental threat. The present study deals with microbial degradation of TBP using Klebsiella pneumoniae S3 isolated from the soil. Diauxic growth curve pattern explains a preferential utilization of TBP. The strain S3 was able to biotransform TBP (1,000 mg L^?1) to dibutyl phosphate within 48 h and showed higher tolerance towards TBP up to 17.0 g L^?1. Toxicity of the parent as well as degraded product was assessed using comet assay. Generation of reactive oxygen species elaborates the oxidative stress imposed upon the bacterial strain by TBP. The antioxidant defense mechanism was studied using various biomarkers namely catalase, glutathione-S-transferase, and superoxide dismutase. The present study describes a faster and eco-friendly alternative for disposal of TBP.     

Biodegradation of dibutyl phosphite by Sphingobium sp. AMGD5 isolated from aerobic granular biomass

In the present study, cultivation of aerobic granular biomass capable of biodegradation of dibutyl phosphite, an organophosphite, and isolation of dibutyl phosphite degrading bacterial strains, are reported for the first time. The strain AMGD5, identified as Sphingobium sp., based on 16S rRNA sequencing, degraded dibutyl phosphite efficiently and utilised it as the sole source of carbon and phosphorus. Microbial degradation of dibutyl phosphite caused a significant decrease in medium pH, leading to cessation of growth and further degradation of dibutyl phosphite. Under buffered conditions, complete degradation of up to 3 mM of dibutyl phosphite was achieved within 60 h. The strain showed almost similar growth pattern when either phosphite or dibutyl phosphite was used as the phosphorous source. A 4-fold enhancement in phosphatase activity was evident in dibutyl phosphite fed cells, implying their role in dibutyl phosphite degradation. Sphingobium sp. AMGD5 can be a potential candidate for bioremediation of dibutyl phosphite contaminated waters or sites.     

Tributyl phosphate degradation by Serratia odorifera

Several strains from tributyl phosphate (TBP)-polluted soils were isolated and screened for their ability to degraded this widely used organophosphorus compound. The most active strain, identified as Serratia odorifera, degrades up to 600 microM TBP (initially present in the medium at 2 mM) during its growth phase, within 8 h from inoculation. However, this bacterium could not utilize TBP as the sole carbon and/or phosphorus source but nevertheless is a good candidate for bioremediation of TBP-polluted industrial sites.     

Optimization of cellulase-free xylanase production by alkalophilic Cellulosimicrobium sp. CKMX1 in solid-state fermentation of apple pomace using central composite design and response surface methodology

Microbial xylanases and associated enzymes degrade the xylans present in lignocellulose in nature. Xylanase production by Cellulosimicrobium sp. CKMX1, isolated from mushroom compost, produced a cellulase-free extracellular endo-1, 4-β-xylanase (EC 3.2.1.8) at 35 °C and pH 8.0. Apple pomace—an inexpensive and abundant source of carbon—supported maximal xylanase activity of 500.10 U/g dry bacterial pomace (DBP) under solid state fermentation. Culture conditions, e.g., type of medium, particle size of carbon source, incubation period, temperature, initial pH, and inoculum size, were optimized and xylanase activity was increased to 535.6 U/g DBP. CMCase, avicelase, FPase and β-glucosidase activities were not detected, highlighting the novelty of the xylanase enzyme produced by CKMX1. Further optimization of enzyme production was carried out using central composite design following response surface methodology with four independent variables (yeast extract, urea, Tween 20 and carboxymethyl cellulose), which resulted in very high levels of xylanase (861.90 U/g DBP). Preliminary identification of the bacterial isolate was made on the basis of morphological and biochemical characters and confirmed by partial 16Sr RNA gene sequencing, which identified CKMX1 as Cellulosimicrobium sp. CKMX1. A phylogenetic analysis based on the 16Sr RNA gene sequence placed the isolate within the genus Cellulosimicrobium, being related most closely to Cellulosimicrobium cellulans strain AMP-11 (97% similarity). The ability of this strain to produce cost-effective xylanase from apple pomace on a large scale will help in the waste management of apple pomace.     

Biodegradation of tributyl phosphate by novel bacteria isolated from enrichment cultures

Tributyl phosphate (TBP) is an organophosphorous compound, used extensively (3000–5000 tonnes/annum) as a solvent for nuclear fuel processing and as a base stock in the formulation of fire-resistant aircraft hydraulic fluids and other applications. Because of its wide applications and relative stability in the natural environment TBP poses the problem of pollution and health hazards. In the present study, fifteen potent bacterial strains capable of using tributyl phosphate (TBP) as sole carbon and phosphorus source were isolated from enrichment cultures. These isolates were identified on the basis of biochemical and morphological characteristics and 16S rRNA gene sequence analysis. Phylogenetic analysis of 16S rRNA gene sequences revealed that two isolates belonged to class Bacilli and thirteen to β and γ-Proteobacteria. All these isolates were found to be members of genera Alcaligenes, Providencia, Delftia, Ralstonia, and Bacillus. These isolates were able to tolerate and degrade up to 5 mM TBP, the highest concentration reported to date. The GC–MS method was developed to monitor TBP degradation. Two strains, Providencia sp. BGW4 and Delftia sp. BGW1 showed respectively, 61.0 ± 2.8% and 57.0 ± 2.0% TBP degradation within 4 days. The degradation rate constants, calculated by first order kinetic model were between 0.0024 and 0.0099 h⁻¹. These bacterial strains are novel for TBP degradation and could be used as an important bioresource for efficient decontamination of TBP polluted waste streams.     

Isolation, identification and characterization of a novel Ralstonia sp. FD-1, capable of degrading 4-fluoroaniline

A gram-negative strain, designated as FD-1, isolated from aerobic activated sludge was capable of metabolizing 4-fluoroaniline (4-FA) as its sole carbon and nitrogen source and energy supply. According to the Biolog GNIII detection method 17 of 71 carbon substrates were easily utilized, while 12 of 23 substrates did not inhibit strain FD-1. The 16S rDNA sequence from strain FD-1 was 99 % similar to Ralstonia sp., suggesting that it belonged to the genus Ralstonia. The optimal conditions for growth and 4-FA degradation were pH 7 and 30 °C. The tolerance to 4-FA were 1,250 mg/L, while the tolerance to salinity was 15 g/L. Catechol 2,3-dioxygenase activity was detected and degradation intermediates were analyzed by liquid chromatography mass spectrometry leading to a proposed degradation pathway and suggesting that extradiol cleavage was involved in 4-FA degradation. This is the first report on the degradation of 4-FA by a bacterium from the Ralstonia genus.     

Influence of ε-caprolactam on growth and physiology of environmental bacteria

ε-Caprolactam was found to have an effect on ecologically important soil bacteria. It inhibited the growth of several Bacillus sp. and Rhizobium sp. but cells of Arthrobacter sp. were able to grow in the presence of caprolactam. Sphingomonas sp. lost its inherent capacity to produce extracellular polymer (EPS) if grown in medium containing caprolactam. In the case of raw domestic sewage, the diversity of native bacteria was diminished in presence of caprolactam. Polluted sea water yielded predominantly one type of caprolactam-degrading bacteria of the genus Achromobacter. These cells efficiently utilized up to 10 g caprolactam/L as the sole source of carbon and nitrogen in synthetic medium even in the presence of 20 g NaCl/L. Compared to cells of Arthrobacter sp., cells of Achromobacter sp. accumulated high amount of 6-aminocaproic acid due to degradation of caprolactam. When using caprolactam as sole source of carbon and nitrogen, Achromobacter cells showed unique physiological ability to produce EPS upon prolonged incubation in solid medium and in broth with low phosphate (C:N:P ratio 100:20:0.05). Hydrolyzed cell-free EPS had glucose as its major component though the only substrate provided in the medium for growth was caprolactam.     

Reduced leaching of the herbicide MCPA after bioaugmentation with a formulated and stored Sphingobium sp.

The use of pesticides on sandy soils and on many non-agricultural areas entails a potentially high risk of water contamination. This study examined leaching of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) after bioaugmentation in sand with differently formulated and stored Sphingobium sp. T51 and at different soil moisture contents. Dry formulations of Sphingobium sp. T51 were achieved by either freeze drying or fluidised bed drying, with high initial cell viability of 67–85 %. Storage stability of T51 cells was related to formulation excipient/carrier and storage conditions. Bacterial viability in the fluidised bed-dried formulations stored at 25 °C under non-vacuum conditions was poor, with losses of at least 97 % within a month. The freeze-dried formulations could be stored substantially longer, with cell survival rates of 50 %, after 6 months of storage at the same temperature under partial vacuum. Formulated and long-term stored Sphingobium cells maintained their MCPA degradation efficacy and reduced MCPA leaching as efficiently as freshly cultivated cells, by at least 73 % when equal amounts of viable cells were used. The importance of soil moisture for practical field bioaugmentation techniques is discussed.     

Lindane degradation by Candida VITJzN04, a newly isolated yeast strain from contaminated soil: kinetic study,enzyme analysis and biodegradation pathway

A new yeast strain was isolated from sugarcane cultivation field which was able to utilize lindane as sole carbon source for growth in mineral medium. The yeast was identified and named as Candida sp. VITJzN04 based on a polyphasic approach using morphological, biochemical and 18S rDNA, D1/D2 and ITS sequence analysis. The isolated yeast strain efficiently degraded 600 mg L^?1 of lindane within 6 days in mineral medium under the optimal conditions (pH 7; temperature 30 °C and inoculum dosage 0.06 g L^?1) with the least half-life of 1.17 days and degradation constant of 0.588 per day. Lindane degradation was tested with various kinetic models and results revealed that the reaction could be described best by first-order and pseudo first-order models. In addition, involvement of the enzymes viz. dechlorinase, dehalogenase, dichlorohydroquinone reductive dechlorinase, lignin peroxidase and manganese peroxidase was noted during lindane degradation. Addition of H₂O₂ in the mineral medium showed 32 % enhancement of lindane degradation within 3 days. Based on the metabolites identified by GC–MS and FTIR analysis, sequential process of lindane degradation by Candida VITJzN04 was proposed. To the best of our knowledge, this is the first report of isolation and characterization of lindane-degrading Candida sp. and elucidation of enzyme systems during the degradation process.     

Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer

Ethyl tert-butyl ether (ETBE) enrichment was obtained by adding contaminated groundwater to a mineral medium containing ETBE as the sole carbon and energy source. ETBE was completely degraded to biomass and CO₂ with a transient production of tert-butanol (TBA) and a final biomass yield of 0.37?±?0.08 mg biomass (dry weight).mg^?1 ETBE. Two bacterial strains, IFP 2042 and IFP 2049, were isolated from the enrichment, and their 16S rRNA genes (rrs) were similar to Rhodococcus sp. (99 % similarity to Rhodococcus erythropolis) and Bradyrhizobium sp. (99 % similarity to Bradyrhizobium japonicum), respectively. Rhodococcus sp. IFP 2042 degraded ETBE to TBA, and Bradyrhizobium sp. IFP 2049 degraded TBA to biomass and CO₂. A mixed culture of IFP 2042 and IFP 2049 degraded ETBE to CO₂ with a biomass yield similar to the original ETBE enrichment (0.31?±?0.02 mg?biomass.mg^?1 ETBE). Among the genes previously described to be involved in ETBE, MTBE, and TBA degradation, only alkB was detected in Rhodococcus sp. IFP 2042 by PCR, and none were detected in Bradyrhizobium sp. IFP 2049.     

Biodegradation of para-nitrophenol by Citricoccus nitrophenolicus strain PNP1T at high pH

A gram-positive bacterium Citricoccus nitrophenolicus (strain PNP1^T, DSM 23311^T, CCUG 59571^T) isolated from a waste water treatment plant was capable of effectively degrading p-nitrophenol (pNP) as a source of carbon, nitrogen and energy for growth. Degradation of pNP required oxygen and resulted in the stoichiometric release of nitrite. Strain PNP1^T also degraded 4-chlorophenol, phenol and salicylate. pNP was degraded at pH values between 6.8 and 10.0 and at temperatures between 15–32 °C. pNP at concentrations up to 150 mg L^?1 were degraded during growth in media at pH ≤ 10, whereas 200 mg L^?1 was completely inhibitory to growth. When incubated in an NH₄Cl-free medium (pH 10) containing both pNP and acetate, pNP is degraded with concomitant release of nitrite which was subsequently assimilated during acetate degradation. Intact cells of strain PNP1^T suspended in NaHCO₃/Na₂CO₃ buffer were able to continuously degrade 200 mg L^?1 pNP over a 40 day period at pH 10.     

Biodegradation of methyl parathion and p-nitrophenol by a newly isolated Agrobacterium sp. strain Yw12

Strain Yw12, isolated from activated sludge, could completely degrade and utilize methyl parathion as the sole carbon, phosphorus and energy sources for growth in the basic salt media. It could also completely degrade and utilize p-nitrophenol as the sole carbon and energy sources for growth in the minimal salt media. Phenotypic features, physiological and biochemical characteristics, and phylogenetic analysis of 16S rRNA sequence showed that this strain belongs to the genus of Agrobacterium sp. Response surface methodology was used to optimize degradation conditions. Under its optimal degradation conditions, 50 mg l⁻¹ MP was completely degraded within 2 h by strain Yw12 and the degradation product PNP was also completely degraded within 6 h. Furthermore, strain Yw12 could also degrade phoxim, methamidophos, chlorpyrifos, carbofuran, deltamethrin and atrazine when provided as the sole carbon and energy sources. Enzymatic analysis revealed that the MP degrading enzyme of strain Yw12 is an intracellular enzyme and is expressed constitutively. These results indicated that strain Yw12 might be used as a potential and effective organophosphate pesticides degrader for bioremediation of contaminated sites.     

Depolymerization and decolorization of kraft lignin by bacterium Comamonas sp. B-9

There is no commercial or industrial-scale process for the remediation of black liquor using microorganisms to date. One of the most important causes is that most microorganisms are not able to use lignin as their principal metabolic carbon or energy source. The bacterial strain Comamonas sp. B-9 has shown remarkable ability to degrade kraft lignin and decolorize black liquor using lignin as its principal metabolic carbon and energy source. This report looks at the depolymerization and decolorization of kraft lignin by Comamonas sp. B-9. The degradation, decolorization, and total carbon removal reached 45, 54, and 47.3 %, respectively, after 7 days treatment. Comamonas sp. B-9 was capable of depolymerizing kraft lignin effectively as analyzed by gel permeation chromatography and decolorization via degrading benzene ring structures as shown using Fourier transform infrared spectroscopy analysis.     

Biodegradation and kinetic analysis of phthalates by an Arthrobacter strain isolated from constructed wetland soil

A bacterial strain C21 isolated from constructed wetland soil was identified as Arthrobacter sp. based on 16S rRNA gene sequence analysis and physio-biochemical characteristics and was capable of utilizing di-n-butyl phthalate (DBP) as a carbon and energy source for growth. Strain C21 can also utilize other phthalates (PAEs) up to a molecular weight of 390.56 and phthalic acid (PA). The biodegradability of these compounds decreased with the increase in the length of phthalate alkyl chains and molecular weight. Kinetic analysis indicated that the strain C21 cell growth on DBP fitted well with Haldane-Andrews’ model (R ²?>?0.98) with μ _max, K _s, and K _i of 0.12/h, 4.2 mg/L, and 204.6 mg/L, respectively. When the initial DBP concentration was lower than 100 mg/L, DBP biodegradation reaction fitted with the first-order kinetics. The results suggested that Arthrobacter strain C21 played an active role in the bioremediation of the wetland contaminated with phthalates.     

Kinetics and pathway of biodegradation of dibutyl phthalate by Pleurotus ostreatus

Dibutyl phthalate (DBP) is a plasticizer, whose presence in the environment as a pollutant has attained a great deal of attention due to its reported association with endocrine system disturbances on animals. Growth parameters, glucose uptake, percentage of removal efficiency (%E) of DBP, biodegradation constant of DBP (k) and half-life of DBP biodegradation (t_1/2) were evaluated for Pleurotus ostreatus grown on media containing glucose and different concentrations of DBP (0, 500 and 1000 mg l^?1). P. ostreatus degraded 99.6 % and 94 % of 500 and 1000 mg of DBP l^?1 after 312 h and 504 h, respectively. The k was 0.0155 h^?1 and 0.0043 h^?1 for 500 and 1000 mg of DBP l^?1, respectively. t_1/2 was 44.7 h and 161 h for 500 and 1000 mg of DBP l^?1, respectively. Intermediate compounds of biodegraded DBP were identified by GC-MS and a DBP biodegradation pathway was proposed using quantum chemical calculation. DBP might be metabolized to benzene and acetyl acetate, the first would be oxidated to muconic acid and the latter would enter into the Krebs cycle. P. ostreatus has the ability to degrade DBP and utilizes it as source of carbon and energy.     

Biodegradation of cefdinir by a novel yeast strain,Ustilago sp. SMN03 isolated from pharmaceutical wastewater

Cefdinir, a semi-synthetic third generation cephalosporin antibiotic being considered as an emerging pollutant, demands removal from aquatic ecosystems. A yeast strain isolated from pharmaceutical wastewater which was identified as Ustilago sp. SMN03 by molecular techniques and was found to be capable of utilizing cefdinir as a sole carbon source. The isolate was found to degrade 81 % of cefdinir within 6 days under optimized conditions viz. pH 6.0, temperature 30 °C, a shaking speed of 120 rpm, an inoculum dosage of 4 % (w/v) and an initial cefdinir concentration of 200 mg L^?1. Kinetic studies revealed that cefdinir degradation followed the pseudo-first order model, a rate constant of 0.222 per day and a half-life period of 3.26 days. Using LC–MS analysis, six novel intermediates formed during the cefdinir degradation were identified and characterized. FT-IR analysis showed that the functional groups ranging from 1,766 to 1,519 cm^?1, characteristic for lactam ring were completely removed during the cefdinir degradation. The opening of the β-lactam ring was one of the major steps in the cefdinir degradation process. Based on the results from the present study, a possible pathway of cefdinir degradation by Ustilago sp. SMN03 was proposed. To the best of our knowledge, this is the first report on microbial degradation of cefdinir by yeast.     

Efficacy of Acinetobacter sp. B9 for simultaneous removal of phenol and hexavalent chromium from co-contaminated system

The present study shows the feasibility of a newly isolated strain Acinetobacter sp. B9 for concurrent removal of phenol and Cr (VI) from wastewater. The experiments were conducted in a batch reactor under aerobic conditions. Initially, when mineral salt solution was used as the culture medium, the strain was found to utilize phenol as sole carbon and energy source while no Cr (VI) removal was observed. However, the addition of glucose as co-carbon source resulted in the removal of both toxicants. This co-removal efficiency of the strain was further improved with nutrient-rich media (NB). Optimum co-removal was determined at 188 mg L^?1 of phenol and 3.5 mg L^?1 of Cr (VI) concentrations at pH 7.0. Strain B9 followed the orthometabolic pathway for phenol degradation. Transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR) studies showed sorption of chromium as one of the major mechanisms for Cr (VI) removal by B9 cells. Acinetobacter sp. B9 was later on checked for bioremediation of real tannery wastewater. After 96 h of batch treatment of tannery effluent containing an initial 47 mg L^?1 phenol and 16 mg L^?1 Cr (VI), complete removal of phenol and 87 % reduction of Cr (VI) were attained, showing high efficiency of the bacterial strain for potential application in industrial pollution control.     

Anaerobic degradation of 2,4-dichlorophenoxyacetic acid by <Emphasis Type="Italic">Thauera</Emphasis> sp. DKT

Thauera sp. strain DKT isolated from sediment utilized 2,4-dichlorophenoxyacetic acid (2,4D) and its relative compounds as sole carbon and energy sources under anaerobic conditions and used nitrate as an electron acceptor. The determination of 2,4D utilization at different concentrations showed that the utilization curve fitted well with the Edward model with the maximum degradation rate as 0.017?±?0.002 mM/day. The supplementation of cosubstrates (glucose, acetate, sucrose, humate and succinate) increased the degradation rates of all tested chemical substrates in both liquid and sediment slurry media. Thauera sp. strain DKT transformed 2,4D to 2,4-dichlorophenol (2,4DCP) through reductive side-chain removal then dechlorinated 2,4DCP to 2-chlorophenol (2CP), 4-chlorophenol (4CP) and phenol before complete degradation. The relative degradation rates by the isolate in liquid media were: phenol?>?2,4DCP?>?2CP?>?4CP?>?2,4D?≈?3CP. DKT augmentation in sediment slurry enhanced the degradation rates of 2,4D and chlorophenols. The anaerobic degradation rates in the slurry were significantly slower compared to the rates in liquid media.     

Isolation and characterization of 3-N-trimethylamino-1-propanol-degrading Rhodococcus sp. strain A2

The aerobic degradation of 3- N -trimethylamino-1-propanol (homocholine) as a sole source of carbon and nitrogen has been found for a Rhodococcus sp. bacterium isolated from soil. The isolate was identified as Rhodococcus sp. strain A2 based on its phenotypic features, physiological and biochemical characteristics, and results of phylogenetic analysis. The washed cells of strain A2 completely degraded homocholine within 6 h, with concomitant formation of several metabolites. Analysis of the metabolites using capillary electrophoresis, fast atom bombardment–MS, and GC–MS showed that trimethylamine was the major metabolite, in addition to β-alanine betaine (β-AB) and trimethylaminopropionaldehyde. Therefore, the possible degradation pathway of homocholine in the isolated strain is through consequent oxidation of the alcohol group (-OH) to aldehyde (-CHO) and acid (-COOH). Thereafter, the cleavage of β-AB C–N bonds yielded trimethylamine and alkyl chain.