Isolation and characterization of a diverse group of phenylacetic acid degrading microorganisms from pristine soil

A diverse range of microorganisms capable of growth on phenylacetic acid as the sole source of carbon and energy were isolated from soil. Sixty six different isolates were identified and grouped according to 16S rRNA gene RFLP analysis. Subsequent sequencing of 16S rDNA from selected strains allowed further characterization of the phenylacetic acid degrading population isolated from soil. Nearly half (30) of the isolates are Bacillus species while the rest of the isolates are strains from a variety of genera namely, Arthrobacter, Pseudomonas, Rhodococcus, Acinetobacter, Enterobacter, Flavobacterium, and Paenibacillus. Sixty-one of the sixty-six strains reproducibly grew in defined minimal liquid culture medium (E2). All strains isolated grew when at least one hydroxylated derivative of phenylacetic acid was supplied as the carbon source, while 59 out of the 61 strains tested, accumulated ortho-hydroxyphenylacetic acid in the assay buffer; when pulsed with phenylacetic acid. Oxygen consumption experiments failed to indicate a clear link between phenylacetic acid and hydroxy-substituted phenylacetic acid in isolates from a broad range of genera.     

Isolation and characterization of mesotrione-degrading Bacillus sp. from soil

Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-Dôme, France) showed that the soil microflora were able to biotransform it.Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods.Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it.     

Isolation and characterization of an Alcaligenes sp. strain DG-5 capable of degrading DDTs under aerobic conditions

In this study, an Alcaligenes sp. strain DG-5 that can effectively degrade dichlorodiphenyltrichloro-ethanes (DDTs) under aerobic conditions was isolated from DDTs-contaminated sediment. Various factors that affect the biodegradation of DDTs by DG-5 were investigated. About 88 %, 65 % and 45 % of the total DDTs were consumed within 120 h when their initial concentrations were 0.5, 5 and 15 mg L^?1, respectively. However, almost no degradation was observed when their concentration was increased to 30 mg L^?1, but the addition of nutrients significantly improved the degradation, and 66 % and 90 % of the total DDTs were degraded at 336 h in the presence of 5 g L^?1 peptone and yeast extract, respectively. Moreover, the addition of 20 mM formate also enhanced the ability of DG-5 to transform DDTs, and its DDT transformation capacity (T_c) value was increased by 1.8 - 2.7 fold for the pure (p,p’-DDT or o,p’-DDT only) and mixed systems (p,p’-DDT, o,p’-DDT, p,p’-DDD and p,p’-DDE). Furthermore, it was found that competitive inhibition in the biodegradation by DDT compounds occurred in the mixed system.     

Isolation and characterization of an Alcaligenes sp. strain DG-5 capable of degrading DDTs under aerobic conditions

In this study, an Alcaligenes sp. strain DG-5 that can effectively degrade dichlorodiphenyltrichloro-ethanes (DDTs) under aerobic conditions was isolated from DDTs-contaminated sediment. Various factors that affect the biodegradation of DDTs by DG-5 were investigated. About 88 %, 65 % and 45 % of the total DDTs were consumed within 120 h when their initial concentrations were 0.5, 5 and 15 mg L?1, respectively. However, almost no degradation was observed when their concentration was increased to 30 mg L?1, but the addition of nutrients significantly improved the degradation, and 66 % and 90 % of the total DDTs were degraded at 336 h in the presence of 5 g L?1 peptone and yeast extract, respectively. Moreover, the addition of 20 mM formate also enhanced the ability of DG-5 to transform DDTs, and its DDT transformation capacity (T(c)) value was increased by 1.8 - 2.7 fold for the pure (p,p'-DDT or o,p'-DDT only) and mixed systems (p,p'-DDT, o,p'-DDT, p,p'-DDD and p,p'-DDE). Furthermore, it was found that competitive inhibition in the biodegradation by DDT compounds occurred in the mixed system.     

Isolation of a selected microbial consortium capable of degrading methyl parathion and p-nitrophenol from a contaminated soil site

A bacterial consortium with the ability to degrade methyl parathion and p-nitrophenol, using these compounds as the only carbon source, was obtained by selective enrichment in a medium with methyl parathion. Samples were taken from Moravia, Medellin; an area that is highly contaminated, owing to the fact that it was used as a garbage dump from 1974 to 1982. Acinetobacter sp, Pseudomonas putida, Bacillus sp, Pseudomonas aeruginosa Citrobacter freundii, Stenotrophomonas sp, Flavobacterium sp, Proteus vulgaris, Pseudomonas sp, Acinetobacter sp, Klebsiella sp and Proteus sp were the microorganisms identified within the consortium. In culture, the consortium was able to degrade 150 mg L?1 of methyl-parathion and p-nitrophenol in 120 h, but after adding glucose or peptone to the culture, the time of degradation decreased to 24 h. In soil, the consortium was also able to degrade 150 mg L?1 of methyl parathion in 120 h at different depths and also managed to decrease the toxicity.     

Isolation and characterization of 1,2,4-trichlorobenzene mineralizing Bordetella sp. and its bioremediation potential in soil

A soil which has been polluted with chlorinated benzenes for more than 25 years was used for isolation of adapted microorganisms able to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB). A microbial community was enriched from this soil and acclimated in liquid culture under aerobic conditions using 1,2,4-TCB as a sole available carbon source. From this community, two strains were isolated and identified by comparative sequence analysis of their 16S-rRNA coding genes as members of the genus Bordetella with Bordetella sp. QJ2-5 as the highest homological strain and with Bordetella petrii as the closest related described species. The 16S-rDNA of the two isolated strains showed a similarity of 100%. These strains were able to mineralize 1,2,4-TCB within two weeks to approximately 50% in liquid culture experiments. One of these strains was reinoculated to an agricultural soil with low native 1,2,4-TCB degradation capacity to investigate its bioremediation potential. The reinoculated strain kept its biodegradation capability: (14)C-labeled 1,2,4-TCB applied to this inoculated soil was mineralized to about 40% within one month of incubation. This indicates a possible application of the isolated Bordetella sp. for bioremediation of 1,2,4-TCB contaminated sites.     

Isolation and characterization of a newly isolated pyrene-degrading Acinetobacter strain USTB-X

The pryene-degradation bacterium strain USTB-X was newly isolated from the polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Beijing Coking Plant, China. The strain was identified as Acinetobacter with respect to its 16S rDNA and morphological and physiological characteristics. The strain was Gram-negative, non-mobile, non-acid-fast, and non-spore-forming, short rods in young culture and 0.8–1.6 μm in diameter and 1.2–2.5 μm long in the stationary phase of growth. Strain USTB-X could utilize pyrene, naphthalene, fluorene, phenanthrene, benzene, toluene, ethylbenzene, ethanol, methanol, and Tween 80 as sole source of carbon and energy. The strain could produce biosurfactants which enhanced the removal of pyrene and could remove 63 % of pyrene with an initial concentration of 100 mg·L^?1 in 16 days without other substrates. Based on the intermediates analyzed by gas chromatography-mass spectrometry, we also deduced the possible metabolic pathway of strain USTB-X for pyrene biodegradation. Results indicated that the strain USTB-X had high potential to enhance the removal of PAHs in contaminated sites.     

氯氰菊酯降解菌CY22-7的分离鉴定及降解特性研究

从采集的多种土壤样品中.获得了19株在3种筛选平板上均生长良好的候选氯氰菊酯降解菌.通过生理生化特性鉴定和16S rDNA序列的测定及比对.将其中的氯氰菊酯降解菌CY22-7鉴定为中华根瘤菌属(Sinorhizobium sp.).同时,对氯氰菊酯降解菌CY22-7的降解特性研究结果表明:(1)氯氰菊酯降解菌CY22-7以5%(体积分数)的接种鼍接种到氯氰菊酯起始质量浓度为100 mg/L的氯氰菊酯乙醇培养基后,于200 r/min、30℃摇床中培养.经过6 d的培养,氯氰菊酯降解菌CY22-7降解了约60%的氯氰菊酯.(2)加人外源营养物质有利于促进氯氰菊酯的降解.其中,葡萄糖和酵母提取物的促进作用最为明显.(3)氯氰菊酯降解菌CY22-7降解氯氰菊酯的最适温度为30℃,最佳pH为6.0.     

Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil

A heavy metal-resistant bacterial strain was isolated from heavy metal-contaminated soils and identified as Burkholderia sp. J62 based on the 16S rDNA gene sequence analysis. The heavy metal- and antibiotic resistance, heavy metal solubilization of the isolate were investigated. The isolate was also evaluated for promoting plant growth and Pb and Cd uptakes of the plants from heavy metal-contaminated soils in pot experiments. The isolate was found to exhibit different multiple heavy metal and antibiotic resistance characteristics. Atomic absorption spectrometer analysis showed increased bacterial solubilization of lead and cadmium in solution culture and in soils. The isolate produced indole acetic acid, siderophore and 1-aminocyclopropane-1-carboxylate deaminase. The isolate also solubilized inorganic phosphate. Inoculation with the isolate was found to significantly (p < 0.05) increase the biomass of maize and tomato plants. Increase in tissue Pb and Cd contents varied from 38% to 192% and from 5% to 191% in inoculated plants growing in heavy metal-contaminated soils compared to the uninoculated control, respectively. These results show that heavy metal-solubilizing and plant growth promoting bacteria are important for plant growth and heavy metal uptake which may provide a new microbial enhanced-phytoremediation of metal-polluted soils.     

一株对硝基苯酚降解菌的筛选鉴定及其降解特性

从受甲基对硫磷污染的土壤中分离筛选得到一株能够以对硝基苯酚(PNP)作为唯一碳源、氮源生长的菌株,命名为TM.经16S rDNA序列分析初步鉴定该菌株为节杆菌(Arthrobacter).考察了该菌株在PNP浓度、盐度(NaCl)、pH、外加碳源(葡萄糖)、外加氮源等因素下对PNP降解特性的影响.结果表明:该菌株对PNP的最大耐受质量浓度为300 mg/L,并在降解的过程中生成NO2-该菌株的耐盐能力可达0.30％(质量分数),其最佳pH为8.在此pH下,200 mg/L的PNP在16h时即可被完全降解,添加0.30％(质量分数)的葡萄糖可使生物量和降解速率达到最大,牛肉膏作为外加氮源最有利于该菌株对PNP的降解.     

Isolation and physiological characterization of the pentachlorophenol degrading bacterium Sphingomonas chlorophenolica

Many chlorophenols tend to persist in the environment, and they may become public health hazards. Among chlorophenols, pentachlorophenol (PCP) is a priority pollutant that has been used widely as a general biocide in commercial wood treatment. Owing to the rapid industrial growth, serious soil and water pollutions by chlorophenols has been reported in Taiwan. In this study, 10 indigenous PCP-degrading bacterial strains were isolated from a PCP-degrading mixed culture, and the potential of both the pure and mixed cultures for PCP degradation compared. Moreover, the physiological characteristics and optimum growth conditions of the PCP-degrading bacteria were investigated. One of the isolated bacterial strains with good potential for PCP degradation was characterized and identified as Sphingomonas chlorophenolica by 16S rDNA gene analysis. The result of the optimum growth temperatures revealed that this organism was a mesophile. The optimum pH for PCP removal by S. chlorophenolica was between 6.9 and 7.6. Increase in concentration of PCP has a negative effect on the biodegradation potential of S. chlorophenolica and PCP concentration above 600 mg l(-1) was inhibitory to its growth. The results of this study indicate that this S. chlorophenolica strain has a better potential for PCP degradation compared to the enriched mixed culture. The physiological characterization of the isolates also indicates the possible application of this strain for bioremediation of sites contaminated with PCP.     

Isolation of a novel Pseudomonas sp from soil that can efficiently degrade polyethylene succinate

Purpose

Polyethylene succinate (PES) is a biodegradable synthetic polymer and therefore widely used as a base material in plastic industry to circumvent the environmental problems related with the non-biodegradability of other polymers like polyethylene. Till date only few organisms have been reported to have the ability to degrade PES. Therefore for better management of PES-related environmental waste, the present study is targeted towards isolating mesophilic organism(s) capable of more efficient degradation of PES.

Results

Strain AKS2 was isolated from soil based on survival on a selection plate wherein PES was used as sole carbon source. Ribotyping and biochemical tests revealed that AKS2 is a new strain of Pseudomonas. Scanning electron and atomic force microscopic analysis of the PES films obtained after incubation with AKS2 confirmed PES-degradation ability of AKS2, wherein an alteration in surface topology was observed. The kinetics of PES weight loss showed that AKS2 degrades PES maximally during its logarithmic growth phase at a rate of 1.65?mg/day. This degradation is mediated by esterase activity and may also involve cell-surface hydrophobicity. It has also been observed that AKS2 is able to degrade PES considerably even in the presence of glucose, which is likely to increase the bioremediation potential of this isolate.

Conclusion

A new strain of Pseudomonas has been isolated from soil that is able to adhere to PES and degrade this polymer efficiently. This organism has the potential to be implemented as a useful tool for bioremediation of PES-derived materials.     

土壤镉胁迫下菲降解菌的筛选及其降解特性研究

以菲和镉为供试物,对沈抚灌区土壤中土著菌进行筛选试验,筛选出一株菲降解菌,命名为W.J,同时测定在不同浓度镉胁迫下,菲为单一碳源时W.J的生长情况.结果表明,在镉胁迫下W.J对菲具有一定的降解能力,镉30 mg/L时,60 h时菲降解率在65%以上.16s rDNA测序比对发现,W.J与Alcaligenes(产碱杆菌属)同源性最高,为99%.通过对W.J生长曲线的测定,发现其对数生长期为0～20 h,这为W.J菌株保存提供了一定的前提条件.高浓度镉在W.J的生长后期对其有明显的毒理效应.     

Isolation and characterization of novel phorate-degrading bacterial species from agricultural soil

Based upon 16S rDNA sequence homology, 15 phorate-degrading bacteria isolated from sugarcane field soils by selective enrichment were identified to be different species of Bacillus, Pseudomonas, Brevibacterium, and Staphylococcus. Relative phorate degradation in a mineral salt medium containing phorate (50 μg ml^?1) as sole carbon source established that all the bacterial species could actively degrade more than 97 % phorate during 21 days. Three of these species viz. Bacillus aerophilus strain IMBL 4.1, Brevibacterium frigoritolerans strain IMBL 2.1, and Pseudomonas fulva strain IMBL 5.1 were found to be most active phorate metabolizers, degrading more than 96 % phorate during 2 days and 100 % phorate during 13 days. Qualitative analysis of phorate residues by gas liquid chromatography revealed complete metabolization of phorate without detectable accumulation of any known phorate metabolites. Phorate degradation by these bacterial species did not follow the first-order kinetics except the P. fulva strain IMBL 5.1 with half-life period (t½) ranging between 0.40 and 5.47 days.     

Isolation, characterization and diuron transformation capacities of a bacterial strain Arthrobacter sp. N2

A bacterial strain able to transform diuron was isolated from a soil by enrichment procedures. Strain isolation was realized by plating on minimal-agarose medium spread with this herbicide and selecting the colonies surrounded by a clear thin halo. One strain was characterized and identified as an Arthrobacter sp. It metabolized diuron and the final transformation product, 3,4-dichloroaniline, was produced in stoichiometric amounts. The transformation of diuron at different concentrations was more efficient in the presence of alternative sources of carbon and nitrogen. The bacterial activity was also evaluated in soil microcosms with a consequent disappearance of diuron and concomitant appearance of 3,4-dichloroaniline, of which the concentration decreased thereafter. Bacterial cells inoculated in the microcosms survived as viable but eventually nonculturable cells.     

一株亚硝酸盐降解菌的分离鉴定与系统发育分析

从水产养殖污泥中分离筛选了一株优良的亚硝酸盐降解菌AQ-3,其在1.0×107 cfu/mL时对50mg/L亚硝酸盐的去除率高达99.47%。通过细菌自动鉴定系统(API ID32GN系统)以及16SrDNA系统发育分析,菌株AQ-3被鉴定为鲍曼氏不动杆菌(Acinetobacter baumannii)(JF751054),其16SrDNA序列与基因库中不动杆菌属菌株的16SrDNA序列有99%的同源性,而且与鲍曼氏不动杆菌菌株14(FJ907197)的亲缘关系最近。此外,菌株AQ-3同时含有nirS基因、nirK基因和norB基因,这些基因对AQ-3高效降解亚硝酸盐具有重要的意义。     

石油污染土壤生物修复菌Z1a-B的分离鉴定与调控效应研究

从山东东营胜利油田附近的石油污染土壤中分离筛选得到一株高效石油降解菌Z1a-B,通过菌落形态及显微镜个体形态观察对其初步鉴定到属,并采用气相色谱/质谱(GC/MS)法分析了Z1a-B的石油降解性能,采用投加石油降解菌、调节土壤N、P含量和优化环境因素等措施,进行了为期60d的石油污染土壤室外自然堆制生物修复实验。结果表明,Z1a-B为链霉菌属白孢类群,其摇瓶培养的石油降解率为66.4%;Z1a-B有着很宽的烷烃降解谱;N、P最佳的添加量组合为KNO32.50g/kg、K2HPO40.35g/kg,即N/P(质量比)为5.57:1.00,此时的石油降解率达63.5%,土壤脱氢酶活性达最高值,为2.99μL/g;石油降解的最佳环境条件为:将石油质量分数为3.3%的100g土样调节pH至8.5后,装入容积为300mL的锥形瓶中灭菌,再接种孢子密度为2.7×108个/mL的菌剂5.5mL,于28℃下进行生物降解,在此条件下的石油降解率可达76.5%;土壤脱氢酶活性的测定结果可以作为检验石油污染土壤生物修复效果的重要指示指标之一;室外自然堆制生物修复实验中,添加菌剂、锯末、秸秆以及N、P后,石油降解率可达69.9%,总体来说,室外自然堆制生物修复是一种投资少、见效快、治理效果较好的石油污染土壤治理方法。     

Isolation and 16S DNA characterization of soil microorganisms from tropical soils capable of utilizing the herbicides hexazinone and tebuthiuron

Six non-fermentative bacteria were isolated from Colombian (South America) and Hawaiian (USA) soils after enrichment with minimal medium supplemented with two herbicides, hexazinone (Hex) and tebuthiuron (Teb). Microscopic examination and physiological tests were followed by partial 16S DNA sequence analysis, using the first 527 bp of the 16S rRNA gene for bacterial identification. The isolated microorganisms (and in brackets, the herbicide that each degraded) were identified as: from Colombia. Methylobacterium organophilum [Teb], Paenibacillus pabuli [Teb], and Micrmbacterium foliorum [Hex]; and from Hawaii, Methylobacterium radiotolerans [Teb], Paenibacillus illinoisensis [Hex], and Rhodococcus equi [Hex]. The findings further explain how these herbicides, which have potential for illicit coca (Erythroxylum sp.) control, dissipate following their application to tropical soils.     

Isolation and characterization of a potential paraffin-wax degrading thermophilic bacterial strain Geobacillus kaustophilus TERI NSM for application in oil wells with paraffin deposition problems

Paraffin deposition problems, that have plagued the oil industry, are currently remediated by mechanical and chemical means. However, since these methods are problematic, a microbiological approach has been considered. The bacteria, required for the mitigation of paraffin deposition problems, should be able to survive the high temperatures of oil wells and degrade the paraffins under low oxygen and nutrient conditions while sparing the low carbon chain paraffins. In this study, a thermophilic paraffinic wax degrading bacterial strain was isolated from a soil sample contaminated with paraffinic crude oil. The selected strain, Geobacillus TERI NSM, could degrade 600mg of paraffinic wax as the sole carbon source in 1000ml minimal salts medium in 7d at 55 degrees C. This strain was identified as Geobacillus kaustophilus by fatty acid methyl esters analysis and 16S rRNA full gene sequencing. G. kaustophilus TERI NSM showed 97% degradation of eicosane, 85% degradation of pentacosane and 77% degradation of triacontane in 10d when used as the carbon source. The strain TERI NSM could also degrade the paraffins of crude oil collected from oil wells that had a history of paraffin deposition problems.     

Isolation and characterization of a mesophilic cellulolytic endophyte Preussia africana from Juniperus oxycedrus

Environmental Science and Pollution Research - The medicinal plant Juniperus oxycedrus is less recognized for the diversity of its fungal endophytes and their potential to produce extracellular...