Potential of hexadecane-utilizing soil-microorganisms for growth on hexadecanol, hexadecanal and hexadecanoic acid as sole sources of carbon and energy

Bacteria and fungi in pristine and oily desert soil samples were counted on inorganic medium aliquots containing 0.5% hexadecane, hexadecanol, hexadecanal or hexadecanoic acid, as sole sources of carbon and energy. It was found that the carbon and energy source most commonly utilized by soil bacteria was the alkane n-hexadecane, and by soil fungi hexadecanoic acid. Representative microorganisms were isolated and identified. The most predominant bacteria in all soil samples belonged to the genera Micrococcus and Pseudomonas; less dominant bacteria belonged to the group of nocardioforms. The most frequent fungal genera were Aspergillus and Penicillium, while Microsporium and Ulocladium were minor fungi. Irrespective of the substrate on which the microbial strains had initially been isolated, the majority of the isolated microorganisms could grow, albeit to a varying degree, on an inorganic medium containing any of the remaining three substrates as sole carbon and energy sources. Bacterial strains preferred the alkane as a carbon and energy source over any of its oxidation products, while fungal strains preferred to grow mainly on the fatty acids. Quantitative analysis by gas liquid chromatography revealed that the predominant bacterial and fungal isolates had a potential for the attenuation of the alkane and its immediate oxidation products in the medium. In view of the continuous release of hydrocarbon oxidation products by oil-utilizing microorganisms in oily environments, it is interesting that the indigenous microflora contribute to the uptake and utilization of all such intermediate compounds, thus, having a potential for efficient self-cleaning and bioremediation of oily soils.     

Complete degradation of butyl benzyl phthalate by a defined bacterial consortium: role of individual isolates in the assimilation pathway

Two bacterial strains, in consortium, were isolated by enrichment techniques from municipal waste-contaminated soil, which utilized butyl benzyl phthalate (BBP) as the sole carbon source. One of the isolates was identified as Arthrobacter sp. strain WY and the other one as Acinetobacter sp. strain FW based on the morphological, nutritional and biochemical characteristics and 16S rRNA sequence analysis. Various metabolites of BBP engendered by Arthrobacter sp. strain WY were isolated and identified by a combination of chromatographic and spectrophotometric analyses, which revealed a pathway involving monobutylphthalate (MBuP), monobenzyl phthalate (MBzP), phthalic acid and protocatechuic acid. The protocatechuic acid in turn was processed by ortho-cleavage dioxygenase to form beta-carboxy-cis,cis-muconate, ultimately leading to the TCA cycle. The Arthrobacter sp. strain WY could not utilize the hydrolyzed alcohols of BBP. On the other hand, the Acinetobacter sp. strain FW, which by itself could not utilize BBP as the sole carbon source, is capable of utilizing the hydrolyzed alcohols of BBP. Benzyl alcohol was found to be metabolized by the Acinetobacter sp. strain FW via benzaldehyde, benzoic acid and catechol. Catechol was further degraded by ortho-cleavage dioxygenase to cis,cis-muconic acid and subsequently to muconolactone leading to beta-ketoadipate pathway. Moreover, the Acinetobacter sp. strain FW metabolized 1-butanol through butyraldehyde and butyric acid leading to the tricarboxylic acid cycle via beta-oxidation pathway. This is the first report on the complete degradation of BBP by a defined consortium describing the role of its individual constituents in the BBP assimilation pathway.     

菌源对多环芳烃降解菌的筛选及降解性能的影响

高效降解菌的筛选对利用生物修复技术有效去除环境中的多环芳烃具有重要意义。分别以石油污染土壤和焦化废水活性污泥为菌源,分离出芘降解菌和混合PAHs(菲、荧蒽和芘)降解菌共14株并对其降解性能进行对比研究。结果表明,筛选得到的菌株分别属于9个菌属,其中2种菌源共有的菌属为Mycobacterium sp.、Ralstonia sp.和Shinella sp.。芘和PAHs的高效降解菌(CP16和CM32)均属于分支杆菌属(Mycobacterium),来源于焦化废水活性污泥;菌株CP16对芘(50mg/L)的7 d降解率为74.99%,CM32对PAHs(菲50 mg/L、荧蒽和芘各10 mg/L)的7 d降解率为100%。因此,以焦化废水活性污泥为菌源更有利于获得高效的多环芳烃降解菌。     

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.     

Characterization of heavy metal-resistant endophytic bacteria from rape (Brassica napus) roots and their potential in promoting the growth and lead accumulation of rape

Two lead (Pb)-resistant endophytic bacteria were isolated from rape roots grown in heavy metal-contaminated soils and characterized. A pot experiment was conducted for investigating the capability of the two isolates to promote the growth and Pb uptake of rape from Pb-amended soil. The two isolates were identified as Pseudomonas fluorescens G10 and Microbacterium sp. G16 based on the 16S rDNA gene sequence analysis. Strains G10 and G16 exhibited different multiple heavy metal and antibiotic resistance characteristics and increased water-soluble Pb in solution and in Pb-added soil. Root elongation assays demonstrated increases in root elongation of inoculated rape seedlings compared to the control plants. Strain G16 produced indole acetic acid, siderophores and 1-aminocyclopropane-1-carboxylate deaminase. Increases in biomass production and total Pb uptake in the bacteria-inoculated plants were obtained compared to the control. The two strains could colonize the root interior and rhizosphere soil of rape after root inoculation.     

红三叶草根际区石油降解菌的筛选及降解性能

从石油污染的土壤红三叶草（nifoliumrepensLinn）根际修复区中分离筛选得到4株以原油作为惟一碳源和能源进行生长繁殖的高效石油降解菌。通过菌落形态、显微镜个体形态观察、生理生化鉴定以及菌株16SrDNA序列分析，初步鉴定4株优势降解菌分别为动性杆菌、藤黄微球菌、蜡状芽孢杆菌和短小芽孢杆菌。采用气相色谱／质谱（GC／MS）法分析4株混合菌对石油烃的降解性能。结果表明：在摇床培养条件下，混合菌54d对总石油烃的生物降解率达到90．50％，较对照高67．72％。随着生物降解时间的延长，石油组分中的正构烷烃、异构烷烃及环烷烃相对总量均呈减小趋势，而芳香烃和其他醇类、醛和酸类的相对含量则有所增加。     

硝化菌的分离及特性分析

从联合脱硫脱氮填料塔中的陶粒上分离出两株硝化菌,命名为NS2和NS5,这2种菌均为革兰氏阴性菌。硝化能力测试结果表明:NS2和NS5能利用亚硝酸盐作为氮源,将亚硝酸盐转化成硝酸盐,硝化速率都达到60%以上。部分长度的16S rDNA序列同源性分析表明,NS2和NS5与Delftia sp.的同源性高达99%,并用MEGA程序对该菌株进行了系统发育进化分析。结合形态观察和生理生化鉴定,初步鉴定NS2,NS5为戴尔福特菌(Delftia sp.)。     

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 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.     

Dimethylphthalate hydrolysis by specific microbial esterase

TWO BACTERIAL STRAINS: Arthrobacter sp. and Sphingomonas paucimobilis were isolated from soil by enrichment cultures using dimethylphthalate (DMP) or monomethylphthalate (MMP) as sole carbon source, respectively. DMP was rapidly transformed by an Arthrobacter sp. culture with formation of MMP and phthalic acid (PA) which is further degraded. This strain was unable to hydrolyse MMP. A mechanism of degradation of DMP was proposed with two ways: DMP-->PA and DMP-->MMP. The S. paucimobilis strain hydrolyses only MMP and a coculture of the two strains allowed a complete degradation of DMP.     

Treatment of cork boiling wastewater using chemical oxidation and biodegradation

Three cultures were enriched from cork boiling wastewater using tannic acid as the selective carbon substrate, at 25 degrees C and pH 7.2, 25 degrees C and pH 4.7 and 50 degrees C and pH 4.7. The enrichment culture obtained at neutral pH was composed of five culturable isolates, whereas from each acidic enrichment two bacterial strains were isolated. Mesophilic isolates were Gram negative bacteria belonging to the genera Klebsiella, Pseudomonas, Stenotrophomonas and Burkholderia. Thermophilic isolates were members of the genus Bacillus. Despite the capability of the enrichment cultures to use tannic acid as single carbon and energy source, those cultures were unable to reduce the total polyphenols or the total organic carbon content of cork boiling wastewater. In order to increase the bioavailability of the organic carbon in cork boiling wastewater, biodegradation was preceded by Fenton oxidation. It was demonstrated that the combined process, using small amounts of Fenton reagents and biodegradative inoculum added almost simultaneously to cork boiling wastewater, leads to TOC reductions of more than 90%.     

New bacterial strain of the genus Ochrobactrum with glyphosate-degrading activity

Thirty bacterial strains with various abilities to utilize glyphosate as the sole phosphorus source were isolated from farm soils using the glyphosate enrichment cultivation technique. Among them, a strain showing a remarkable glyphosate-degrading activity was identified by biochemical features and 16S rRNA sequence analysis as Ochrobactrum sp. (GDOS). Herbicide (3 mM) degradation was induced by phosphate starvation, and was completed within 60 h. Aminomethylphosphonic acid was detected in the exhausted medium, suggesting glyphosate oxidoreductase as the enzyme responsible for herbicide breakdown. As it grew even in the presence of glyphosate concentrations as high as 200 mM, Ochrobactrum sp. could be used for bioremediation purposes and treatment of heavily contaminated soils.     

The bacterial metabolism of 4,4′-dichlorobiphenyl,and its suppression by alternative carbon sources

The metabolism of 4,4′-dichlorobiphenyl by mixed cultures of bacteria, isolated from activated sludge, was studied in shake cultures and in soil, both in presence and absence of alternative carbon sources. When 4,4′-dichlorobiphenyl was used as sole carbon source, 4-chlorobenzoic acid and 4,4′-dichloro-2,3-biphenyldiol could be isolated from the culture medium. Polar metabolites however, could not be detected in soil and in media in which alternative carbon sources such as glucose, glycerol, peptone, yeast-extract, humic acid or activated sludge were present. No hydroxylated or carboxylic acid derivatives could be isolated when 2,4′, 5-tri-, 2,2′,5,5′,-textra-, 2,2′,3,4,5′-penta-, 2,2′,3,4,5,5′-hexa- and decachlorobiphenyl were used as the sole carbon sources for incubation with bacteria in shake culture.     

Biodegradation of aromatic hydrocarbons by Haloarchaea and their use for the reduction of the chemical oxygen demand of hypersaline petroleum produced water

Ten halophilic Archaea (Haloarchaea) strains able to degrade aromatic compounds were isolated from five hypersaline locations; salt marshes in the Uyuni salt flats in Bolivia, crystallizer ponds in Chile and Cabo Rojo (Puerto Rico), and sabkhas (salt flats) in the Persian Gulf (Saudi Arabia) and the Dead Sea (Israel and Jordan). Phylogenetic identification of the isolates was determined by 16S rRNA gene sequence analysis. The isolated Haloarchaea strains were able to grow on a mixture of benzoic acid, p-hydroxybenzoic acid, and salicylic acid (1.5 mM each) and a mixture of the polycyclic aromatic hydrocarbons, naphthalene, anthracene, phenanthrene, pyrene and benzo[a]anthracene (0.3 mM each). Evaluation of the extent of degradation of the mixed aromatic hydrocarbons demonstrated that the isolates could degrade these compounds in hypersaline media containing 20% NaCl. The strains were shown to reduce the COD of hypersaline crude oil reservoir produced waters significantly beyond that achieved using standard hydrogen peroxide treatment alone.     

Improvement of rape (Brassica napus) plant growth and cadmium uptake by cadmium-resistant bacteria

This study focuses on the screening of cadmium-resistance bacterial strains from heavy metal-polluted soils to examine their plant growth promotion and cadmium uptake in rape (Brassica napus). A large number of bacteria were isolated from heavy metal-polluted soil in Nanjing, China. Thirty isolates showing cadmium-resistance on Cd-amended medium were selected and evaluated for their potential to solubilize cadmium carbonate in solution culture. Atomic absorption spectrometer analysis showed variable amounts of water-soluble Cd (ranging from 24 to 117 mg l(-1)) released by the cadmium-resistant bacterial strains from cadmium carbonate. Qualitative analysis confirmed the presence of indole acetic acid as the auxin in the culture of these cadmium-resistant bacterial strains. Root elongation assay conducted on rape under gnotobiotic conditions demonstrated increases (up to 31%) in root elongation of inoculated rape seedlings compared to the control plants. Based upon cadmium-resistance, bio-activation of CdCO3 and growth-promoting activity, three isolates were selected for promoting plant growth and uptake of cadmium from cadmium-amended soil in pot experiments. Inoculation with the isolates was found to increase root dry weight (ranging from 8% to 20%) and shoot dry weight (ranging from 6% to 25%) of rape. An increase in cadmium content varying from 16 to 74%, compared to the non-inoculated control, was observed in rape plants cultivated in soil treated with 100 mgCd kg(-1) (as CdCl2) and inoculated with the isolates. The bacterial isolates were also able to colonize and develop in the rhizosphere soil of rape after root inoculation.     

Biodegradation of s-triazine herbicide atrazine by Enterobacter cloacae and Burkholderia cepacia sp. from long-term treated sugarcane-cultivated soils in Kenya

In this study soils from sugarcane-cultivated fields were screened for bacterial species capable of atrazine (6-chloro-N²-ethyl-N⁴-isopropyl-1,3,5-triazine-2,4-diamine) degradation due to long exposure of the soils to this herbicide. To enrich for atrazine degraders, Minimal Salt Medium containing atrazine as the sole N source and glucose as the C source was inoculated with soils impacted with this herbicide and incubated. Bacterial growth was monitored by measuring optical density. The degradation of atrazine was followed by measuring residual atrazine in liquid cultures over a given time period by high performance liquid chromatography. Bacterial strains isolated from the enrichment cultures were characterized by biochemical tests and identified by 16S rRNA gene sequencing. Two bacterial strains coded ISL 8 and ISL 15 isolated from two different fields were shown to have 94 and 96% 16S rRNA gene sequence similarity to Burkholderia cepacia respectively. Another bacterial sp., ISL 14 was closely related to Enterobacter cloacae with a 96% 16S rRNA gene sequence similarity. There was not much difference between the extents of atrazine degradation by the enrichment cultures with communities (79–82% applied amount) from which pure strains were isolated and the pure strains themselves in liquid cultures that showed a degradation of 53–83% of applied amount. The study showed existence of bacterial strains in different sugarcane-cultivated fields which can use atrazine as a nitrogen source. The bacterial strains isolated can be used to enhance the degradation of atrazine in contaminated soils where atrazine is still considered to be recalcitrant.     

Biodegradation of s-triazine herbicide atrazine by Enterobacter cloacae and Burkholderia cepacia sp. from long-term treated sugarcane-cultivated soils in Kenya

In this study soils from sugarcane-cultivated fields were screened for bacterial species capable of atrazine (6-chloro-N2-ethyl-N?-isopropyl-1,3,5-triazine-2,4-diamine) degradation due to long exposure of the soils to this herbicide. To enrich for atrazine degraders, Minimal Salt Medium containing atrazine as the sole N source and glucose as the C source was inoculated with soils impacted with this herbicide and incubated. Bacterial growth was monitored by measuring optical density. The degradation of atrazine was followed by measuring residual atrazine in liquid cultures over a given time period by high performance liquid chromatography. Bacterial strains isolated from the enrichment cultures were characterized by biochemical tests and identified by 16S rRNA gene sequencing. Two bacterial strains coded ISL 8 and ISL 15 isolated from two different fields were shown to have 94 and 96% 16S rRNA gene sequence similarity to Burkholderia cepacia respectively. Another bacterial sp., ISL 14 was closely related to Enterobacter cloacae with a 96% 16S rRNA gene sequence similarity. There was not much difference between the extents of atrazine degradation by the enrichment cultures with communities (79-82% applied amount) from which pure strains were isolated and the pure strains themselves in liquid cultures that showed a degradation of 53-83% of applied amount. The study showed existence of bacterial strains in different sugarcane-cultivated fields which can use atrazine as a nitrogen source. The bacterial strains isolated can be used to enhance the degradation of atrazine in contaminated soils where atrazine is still considered to be recalcitrant.     

Influence of metal resistant-plant growth-promoting bacteria on the growth of Ricinus communis in soil contaminated with heavy metals

The metal resistant-plant growth-promoting bacterial (PGPB) strains PsM6 and PjM15 isolated from a serpentine soil were characterized as Pseudomonas sp. and Pseudomonas jessenii, respectively, on the basis of their morphological, physiological, biochemical characteristics and 16S rDNA sequences. Assessment of plant growth-promoting parameters revealed the intrinsic ability of the strains for the utilization of 1-aminocyclopropane-1-carboxylic acid as the sole N source, solubilization of insoluble phosphate and production of indole-3-acetic acid (IAA). Further, a pot experiment was conducted to elucidate the effects of inoculating metal resistant PGPB on the plant growth and the uptake of Ni, Cu and Zn by Ricinus communis. Inoculation of Pseudomonas sp. PsM6 or P. jessenii PjM15 increased the shoot and root biomass of R. communis grown in non-contaminated and contaminated soil. However, the maximum biomass was observed in the plants inoculated with strain PjM15. This effect can be attributed to the solubilization of phosphate and production of IAA. Inoculation of Pseudomonas sp. PsM6 and PjM15 did not greatly alter the organ metal concentrations except Zn which concentration was higher in root, stem and leaf of inoculated plants. The results of metal extraction with PGPB strains showed that PsM6 was more efficient at solubilizing Zn than PjM15, and that PjM15 was better at solubilising Ni and Cu than PsM6. Owing to its wide action spectrum, the metal resistant PGPB could serve as an effective metal sequestering and growth-promoting bioinoculant for plants in metal-stressed soil. The present study has provided a new insight into the phytoremediation of metal-contaminated soil.     

Degradation and metabolism of hexazinone by two isolated bacterial strains from soil

Two hexazinone-degrading bacterial strains were isolated from soil by enrichment culture technique, and identified as Pseudomonas sp. and Enterobacter cloacap. The two purified isolates, designated as WFX-1 and WFX-2, could rapidly degrade hexazinone with a half-life of 3.08 days and 2.95 days in mineral salt medium (MSM), while their mixed bacterial culture was found to degrade hexazinone, at an initial concentration of 50 microg/ml, by enhancing 2.3-fold over that when the isolates were used alone. Two microbial metabolites (A and D) were obtained by preparative TLC and identified on the basis of the spectral data of IR, 1H NMR and HPLC-ESI-MS, but both of them were known products as they had been reported in soil and vegetation metabolites of hexazinone. However, metabolites B and C were new degradates, whose molecular weights (MW) were 157 and 156, respectively, being reported from microbial metabolism for the first time.     

Biosynthesis of polyhydroxyalkanoate by Gamma proteobacterium WD-3 from volatile fatty acids

The production of copolymers of poly-β-hydroxyalkanoates (PHA) is generally a high cost process. To reduce the production costs, inexpensive carbon sources such as volatile fatty acids (VFAs) from acidified wastewater can be used. Therefore, isolation of bacterial strains that can produce PHA copolymers using VFAs as a sole carbon source would be a beneficial alternative. In this study, a strain of PHA accumulating bacterium was isolated from the wastewater treatment plant of a soybean processing facility in Harbin. The strain was identified as γ-proteobacterium according to its 16S rDNA information and was originally named as strain WD-3. The strain accumulated a mass of PHA up to 45% of its dry cell weight when it was cultured under the optimum fermentation condition in this study when butyrate was used as the carbon source. In addition, WD-3 could synthesize PHA copolymers of poly-hydroxybutyrate and poly-hydroxyvalerate (PHV) either from C-even substrates or from C-odd substrates, and one-third of the copolymer was PHV. Results from this study demonstrated that small molecule organic acids can be used by the strain of WD-3 as the carbon source for growth and PHA production. The maximum PHA yield in the study was 0.45 g g⁻¹ dry cell.