Isolation of Marine Bacteria by In Situ Culture on Media-Supplemented Polyurethane Foam

Polyurethane foam (PUF) supplemented with various agar media was used in situ to trap marine bacteria and it consequently provided a substrate on which they could be cultivated while exposed to natural seawater in the coral reef area. The bacterial population on the PUF blocks was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments. Changing the composition of the cultivation medium in the PUF blocks and selecting different sampling sites resulted in different bacteria being detected on the PUF blocks. For example, iron-utilizing (IU) bacteria, siderophore-producing (SP) bacteria, and petroleum-degrading (PD) bacteria were isolated from PUF blocks and it was discovered that IU and SP contained iron and PD contained hydrocarbon. This method opens up the possibility for isolating novel and useful marine bacteria.     

Rhodococcus sp. F92 immobilized on polyurethane foam shows ability to degrade various petroleum products

This work reports on the immobilization and performance of a hydrocarbon-degrading microorganism on polyurethane foam (PUF) in the bioremediation of petroleum hydrocarbons. The ability of four different microorganisms to immobilize on PUF and to degrade various petroleum products (Arabian light crude (ALC), Al-Shaheen crude (ASC), diesel and oil slops) was assessed by measuring the n-alkane fraction remaining in the petroleum products over time. A Rhodococcus sp. (designated as F92) had the highest number of immobilized viable cells (10(9) cells per cm3 PUF) and a maximum attachment efficiency of 90% on PUF of a density of 14 kg/m3. Scanning electron microscopy showed the presence of extracellular structures that could play an important role in the immobilization of F92 on PUF. Analysis by GC-MS revealed that both free and immobilized F92 cells were able to degrade approximately 90% of the total n-alkanes in the petroleum products tested within 1 week at 30 degrees C. Rhodococcus sp. F92 was efficiently immobilized onto PUF and the immobilized cells were able to degrade a variety of petroleum products such as ALC, ASC, diesel and oil slops. The results suggest the potential of using PUF-immobilized Rhodococcus sp. F92 to bioremediate petroleum hydrocarbons in an open marine environment.     

Biodegradation of Carbofuran phenol by free and immobilized cells of <Emphasis Type="Italic">Klebsiella pneumoniae</Emphasis> ATCC13883T

The Klebsiella sp. strain ATCC13883T capable of degrading carbofuran phenol (2,3-dihydro-2,2-dimethylbenzofuran-7-ol) has been separated from the soil by enrichment culture technique and immobilized in various, namely polyurethane foam (PUF), polyacrylamide, alginate, agar and alginate-bentonite clay-powdered activated charcoal (PAC). The degradation rates of 20 and 30 mM carbofuran phenol by free and immobilized cells in batch and semi-continuous shaken cultures were compared. The PUF-immobilized cells achieved higher degradation rates in a shorter time than freely suspended cells and the cells immobilized in polyacrylamide, alginate and agar. The PUF- and alginate-bentonite clay-PAC-immobilized cells could be reused for more than 36 cycles, polyacrylamide-entrapped cells for 20 cycles and alginate-bentonite-PAC 28 cycles, without losing any degradation capacity and showed better tolerance to pH, temperature and concentration changes than free cells. These results showed that cells immobilized in modified alginate-bentonite-PAC immobilizers tolerated and completely degraded carbofuran phenol at initial concentrations of 20 and 30 mM and also higher. Such a bacterial strain could be used for bioremediation of environments contaminated with phenolic compounds.     

Use of microorganism-immobilized polyurethane foams to absorb and degrade oil on water surface

Highly oil-absorbent polyurethane foam (PUF) materials were obtained by polymerizing polyether polyol mixture and carbodiimide-modified d-methyl diisocyanate in a weight ratio of 10:2. The foam materials were prepared to contain inorganic nutrients (slow-release fertilizer; SRF) and oil-degrading yeast cells, Yarrowia lipolytica 180, to be applied for removal of oil films on surface waters through absorption and biodegradation after oil spills. PUFs absorbed 7–9 times their own weight of Arabian light crude oil and the oil absorbency appeared to improve as the ratio of surface area to foam weight increased. PUFs showed excellent floatability which was maintained for more than 6 months in sea water, and less than 5% of the absorbed oil was released when the foams were left on water for more than 10 days. For immobilization of yeast cells into PUFs, various immobilization techniques were tested to compare their oil degrading ability and the maintenance thereof. All immobilized cells showed oil degrading abilities as good as those of free cells immediately after the preparation of PUFs, however, the activity of chitin-immobilized cells remained at a high level for the longest period of preservation. The high efficiency of oil absorption and oil degradation by PUF-immobilized yeast cells suggested that PUF-immobilized cells have a high potential as a bioremediation technique for the treatment of oil films on surface waters. Received: 27 September 1999 / Received revision: 6 March 2000 / Accepted: 17 March 2000     

Enhanced plasmid stability and production of hEGF by immobilized recombinant E. coli JM101

Recombinant Escherichia coli JM101 was immobilized with porous polyurethane foam (PUF) particle as supporter matrix for human epidermal growth factor (hEGF) production. Flask culture showed that cell immobilization in PUF can improve cell growth and hEGF expression. A bubble column and a three-phase fluidized bed bioreactor by self-design was further applied to produce hEGF, respectively. The results demonstrated that PUF is a feasible immobilized supporter material with good biocompatibility. Immobilization could also decrease the probability for segregational plasmid loss and overgrowth of plasmid-free cells. Cell density, plasmid stability and hEGF productivity were higher than those without the foam matrix, respectively. hEGF productivity was enhanced from 8.73 mg/l h of free-culture to 11.4 mg/l h of immobilized cultivation.     

Effect of Substrate on the Fatty Acid Composition of Hydrocarbon-utilizing Microorganisms

The fatty acid pattern in three hydrocarbon-utilizing bacteria during growth on various substrates was examined. The predominant fatty acids in acetate-grown cells were C(16), C(16:1), C(18:1), and Br-C(19) and the major fatty acids in propane-grown cells were C(15), C(17), C(17:1), C(18:1), and Br-C(18). When one organism (Mycobacterium sp. strain OFS) was grown on the n-alkanes from C(13) to C(17), the major fatty acid in the cells was of the same chain length as the substrate. Studies on the incorporation of acetate into the cellular fatty acids of microorganisms growing on C(15) and C(17)n-alkanes suggest that the oxidative products of the substrate are incorporated into the cellular fatty acids without degradation to acetate.     

Phylogenetic analysis of long-chain hydrocarbon-degrading bacteria and evaluation of their hydrocarbon-degradation by the 2,6-DCPIP assay

Thirty-six bacteria that degraded long-chain hydrocarbons were isolated from natural environments using long-chain hydrocarbons (waste car engine oil, base oil or the c-alkane fraction of base oil) as the sole carbon and energy source. A phylogenetic tree of the isolates constructed using their 16S rDNA sequences revealed that the isolates were divided into six genera plus one family (Acinetobacter, Rhodococcus, Gordonia, Pseudomonas, Ralstonia, Bacillus and Alcaligenaceae, respectively). Furthermore, most of the isolates (27 of 36) were classified into the genera Acinetobacter, Rhodococcus or Gordonia. The hydrocarbon-degradation similarity in each strain was confirmed by the 2,6-dichlorophenol indophenol (2,6-DCPIP) assay. Isolates belonging to the genus Acinetobacter degraded long-chain normal alkanes (n-alkanes) but did not degrade short-chain n-alkanes or cyclic alkanes (c-alkanes), while isolates belonging to the genera Rhodococcus and Gordonia degraded both long-chain n-alkanes and c-alkanes.     

Laccase production using Pleurotus ostreatus 1804 immobilized on PUF cubes in batch and packed bed reactors: influence of culture conditions

The feasibility of laccase production by immobilization of Pleurotus ostreatus 1804 on polyurethane foam (PUF) cubes with respect to media composition was studied in both batch and reactor systems. Enhanced laccase yield was evidenced due to immobilization. A relatively high maximum laccase activity of 312.6 U was observed with immobilized mycelia in shake flasks compared to the maximum laccase activity of free mycelia (272.2 U). It is evident from this study that the culture conditions studied, i.e. biomass level, pH, substrate concentration, yeast extract concentration, Cu2+ concentration, and alcohol nature, showed significant influence on the laccase yield. Gel electrophoretic analysis showed the molecular weight of the laccase produced by immobilized P. ostreatus to be 66 kDa. The laccase yield was significantly higher and more rapid in the packed bed reactor than in the shake flask experiments. A maximum laccase yield of 392.9 U was observed within 144 h of the fermentation period with complete glucose depletion.     

Isolation of Eikenella corrodens in a General Hospital

The carbon source markedly influenced the qualitative and quantitative composition of cellular hydrocarbons in Cladosporium resinae. Total lipid and hydrocarbon content was greater in cells grown on n-alkanes than in cells grown on glucose or glutamic acid. Glucose-grown cells contained a spectrum of aliphatic hydrocarbons from C(7) to C(36); pristane and n-hexadecane comprised 98% of the total. Cells grown on glutamic acid contained C(7) to C(23) hydrocarbons; n-tridecane, n-tetradecane, n-hexadecane, and pristane made up 74% of the total. n-Decane-grown cells yielded C(8) to C(32) compounds, and n-hexadecane (96%) was the major hydrocarbon. Cells grown on individual n-alkanes from C(11) to C(15) all contained C(11) to C(28) hydrocarbons, and cells grown on n-hexadecane contained C(11) to C(32) hydrocarbons. In n-undecane-grown cells, n-hexadecane and pristane made up 92% of the total, but in cells grown on C(12) to C(16)n-alkanes the major cellular hydrocarbon was the one on which the cells were grown. This suggests that cells cultured on n-alkanes of C(12) or longer accumulate n-alkanes prior to oxidizing them.     

Biodegradation of hydrocarbon contamination by immobilized bacterial cells

This study examined the capacity of immobilized bacteria to degrade petroleum hydrocarbons. A mixture of hydrocarbon-degrading bacterial strains was immobilized in alginate and incubated in crude oil-contaminated artificial seawater (ASW). Analysis of hydrocarbon residues following a 30-day incubation period demonstrated that the biodegradation capacity of the microorganisms was not compromised by the immobilization. Removal of n-alkanes was similar in immobilized cells and control cells. To test reusability, the immobilized bacteria were incubated for sequential increments of 30 days. No decline in biodegradation capacity of the immobilized consortium of bacterial cells was noted over its repeated use. We conclude that immobilized hydrocarbon-degrading bacteria represent a promising application in the bioremediation of hydrocarbon-contaminated areas.     

A Mycobacterium strain with extended capacities for degradation of gasoline hydrocarbons

A bacterial strain (strain IFP 2173) was selected from a gasoline-polluted aquifer on the basis of its capacity to use 2,2, 4-trimethylpentane (isooctane) as a sole carbon and energy source. This isolate, the first isolate with this capacity to be characterized, was identified by 16S ribosomal DNA analysis, and 100% sequence identity with a reference strain of Mycobacterium austroafricanum was found. Mycobacterium sp. strain IFP 2173 used an unusually wide spectrum of hydrocarbons as growth substrates, including n-alkanes and multimethyl-substituted isoalkanes with chains ranging from 5 to 16 carbon atoms long, as well as substituted monoaromatic hydrocarbons. It also attacked ethers, such as methyl t-butyl ether. During growth on gasoline, it degraded 86% of the substrate. Our results indicated that strain IFP 2173 was capable of degrading 3-methyl groups, possibly by a carboxylation and deacetylation mechanism. Evidence that it attacked the quaternary carbon atom structure by an as-yet-undefined mechanism during growth on 2,2,4-trimethylpentane and 2,2-dimethylpentane was also obtained.     

Characterization of the nitrobenzene-degrading strain Pseudomonas sp. a3 and use of its immobilized cells in the treatment of mixed aromatics wastewater

A bacterial strain Pseudomonas sp. a3 capable of degrading nitrobenzene, phenol, aniline, and other aromatics was isolated and characterized. When nitrobenzene was degraded, the release of NH(4) (+) was detected, but not of NO(2) (-). This result implied that nitrobenzene might have a partial reductive metabolic pathway in strain a3. However, aniline appeared as one of the metabolites during the aerobic degradation of nitrobenzene. Moreover, the appearance of 2-aminophenol during aniline degradation by strain a3 indicated that novel initial reactions existed during the degradation of nitrobenzene and aniline by strain a3. Strain a3 was immobilized in the mixed carrier of polyvinyl alcohol and sodium alginate to improve its degrading efficiency. The optimal concentrations of polyvinyl alcohol and sodium alginate in the mixed carrier were 9 and 3 %, respectively. The immobilized cells had stable degradation activity and good mechanical properties in the recycling tests. The immobilized cells also exhibited higher tolerances in acidic (pH 4-5) and highly saline (10 % NaCl) environments than those of free cells. The biodegradation of nitrobenzene mixed with aniline and phenol using immobilized cells of Pseudomonas sp. a3 was also greatly improved compared with those of free cells. The immobilized cells could completely degrade 300 mg L(-1) nitrobenzene within 10 h with 150 mg L(-1) aniline and 150 mg L(-1) phenol. This result revealed that the immobilized cells of Pseudomonas sp. a3 could be a potential candidate for treating nitrobenzene wastewater mixed with other aromatics.     

石油降解菌株的分离鉴定及降油特性

从甘肃华庆油田污染严重的土壤中采样,通过富集培养、多次筛选分离得到1株优势菌F1。依据生理生化特征和16S rDNA序列将菌株F1鉴定为白色类诺卡氏菌(Nocardioides albus)。GS-MC结果表明,等量原油经F1菌株降解前、后,表现出先降解高碳数正构烷烃为低碳数正构烷烃;高碳数正构烷烃中奇数碳向偶数碳正构烷烃演化规律;平均降油率为64%,F1菌株能较好地促使五环三萜类化合物立体构型中不稳定构型向稳定性构型转化。F1菌株在含油浓度0.3%、0.5%、1.0%土样中降解石油烃的半衰期分别为17.2、18.2、23.7 d,42 d后均达到78%以上。     

A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence

PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5′ end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.     

Fatty Acid Composition of Cladosporium resinae Grown on Glucose and on Hydrocarbons

Cladosporium resinae was grown in submerged cultures on glucose; on Jet-A commercial aviation fuel; and on a series of n-alkanes, n-decane through n-tetradecane. Cell yield was greatest on glucose and least on Jet-A; n-alkanes were intermediate. Among n-alkanes cell yield decreased as chain length increased, except for n-dodecane, which supported less growth than n-tridecane or n-tetradecane. The total fatty acids of stationary-phase cells were analyzed by gas-liquid chromatography. In all cases the predominant fatty acids were 16:0, 18:1, and 18:2. The fatty acid composition of glucose-grown cells was similar to that of hydrocarbon-grown cells. Cells grown on n-tridecane or n-tetradecane yielded small amounts of acids homologous to the carbon source, but a similar correlation was not noted for n-decane, n-undecane, or n-dodecane. Cells grown on n-undecane or n-tridecane contained more odd-carbon fatty acids than cells grown on the other substrates, and the effect was more pronounced in n-tridecane-grown cells. Thus, the fatty acids of this organism are derived chiefly from de novo synthesis rather than from direct incorporation of oxidized hydrocarbons. The extent of direct incorporation increases as the chain length of the hydrocarbon growth substrate is increased.     

多环芳烃降解菌筛选及其降解特性

通过选择性富集培养,从辽河油田稠油污染土壤4号土样中,获得了能以高浓度菲(2000mg·L^-1)为唯一碳源和能源快速生长的优势菌系和优良菌株ZL5．16S rDNA核苷酸序列分析表明,ZL5菌株归类于鞘氨醇单胞菌属,分得的菌系和菌株有较强的降解菲能力,120h混合菌系降解了投加菲的95．28％,菌株降解了69．24％,但它们对芘的降解能力均较低,外加碳源葡萄糖可提高菌系和菌株的菲、芘降解能力,加量多。提高幅度大,但超过一定量。降解速率开始下降,表现出抑制效应。所以,应用时需控制适宜的浓度。     

Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by <Emphasis Type="Italic">Sphingomonas</Emphasis> sp. strain PheB4

The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate PAHs compared to the PMSM-grown culture. The concentrations of PAH metabolites were also lower in NB-grown culture than in PMSM-grown culture, suggesting that NB-grown culture removed metabolites at a faster rate, particularly, for metabolites produced from cometabolic degradation of a binary mixture of PAHs. Cometabolic pathways of single PAH (anthracene, fluorene, or fluoranthene) in NB-grown culture showed similarity to that in PMSM-grown culture. However, cometabolic pathways of mixed PAHs were more diverse in NB-grown culture than that in PMSM-grown culture. These results indicated that nutrient rich medium was effective in enhancing cometabolic degradation of mixed PAHs concomitant with a rapid removal of metabolites, which could be useful for the bioremediation of mixed PAHs contaminated sites using Sphingomonas sp. strain PheB4.     

Enhanced degradation of naphthalene by immobilization of Pseudomonas sp. strain NGK1 in polyurethane foam

A Pseudomonas sp. strain NGKI (NCIM 5120) capable of degrading naphthalene was immobilized in polyurethane foam. The naphthalene-degrading activity of the freely suspended cells was compared with that of immobilized cells in batches in shaken culture and in a continuous culture system in a packed-bed reactor. Increasing concentrations of naphthalene were better tolerated and more quickly degraded by immobilized cell cultures than by free cells. An initial naphthalene concentration of 25 mM was completely degraded by freely suspended cells (4 x 10(10) cfu ml(-1)) and polyurethane-foam-immobilized cells (0.8-1 x 10(12) cfu g(-1) foam cubes) after 4 days and 2 days of incubation, respectively. Free cells degraded a maximum of 30 mM naphthalene after 4 days of incubation with 50 mM naphthalene, and no further degradation was observed even after 15 days of incubation, whereas foam-immobilized cells brought about the complete degradation of 50 mM initial naphthalene after 6 days of incubation. Furthermore, with 25 mM naphthalene, the polyurethane-foam-immobilized cells were re-used 45 times over a period of 90 days without losing naphthalene-degrading activity. By contrast, with the same amount of naphthalene, alginate-, agar-, and polyacrylamide-entrapped cells could be reused for 18, 12, and 23 times over a period of 44, 28, and 50 days, respectively. During continuous degradation in a packed-bed reactor, foam-immobilized cells degraded 80 mM naphthalene at a rate of 150 ml(-1) h(-1). With the same flow rate and 40 mM naphthalene, this system operated efficiently and continuously for about 120 days, whereas the packed-bed reactor with alginate-, agar-, and polyacrylamide-entrapped cells could be operated only for 45, 40, and 60 days respectively. Thus, more efficient degradation of naphthalene could be achieved by immobilizing cells of Pseudomonas sp. strain NGK1 in polyurethane foam, rather than in the other matrices tested.     

Mobility and Persistence of Petroleum Hydrocarbons in Peat Soils of Southeastern Mexico

Spilled crude petroleum from oil wells contains numerous hydrocarbons, some of which are toxic and threaten life. We have studied the mobility and persistence of hydrocarbons in waterlogged soils that contain large proportions of fermented organic matter (Histosols) and large concentrations of dissolved organic carbon (DOC) in the State of Tabasco, Mexico. We sampled soil and phreatic water at sites polluted by oil spills for several decades, as well as at sites that had only recently (few weeks) been polluted, and compared their hydrocarbon contents with those of unaffected sites in the same area. Samples were analyzed for 16 non-alkylated polyaromatic hydrocarbons (PAHs) and n-alkanes from nC9 to nC34. The spilled hydrocarbons had remained predominantly in the organic surface horizons of the soil where spillage occurred; there was little evidence of movement within the soil. The fraction of low molecular weight compounds was larger at sites of recent spills than where spills happened several decades ago. Nevertheless, sites of old spills still contained large concentrations of hydrocarbons, among which those of low molecular weight represented from 30 to 49% of total PAHs and from 50 to 84% of total n-alkanes, indicating that volatilization or microbial degradation is slow in these soils. In the peat horizons the measured organic carbon partition coefficients (K _oc ) for the higher molecular weight PAHs were consistently smaller than those estimated by empirical equations by up to two orders of magnitude. The dissolved organic carbon of these peat soils seems to influence this behavior. At sites of old spills, partition coefficients for the PAHs were larger than at sites of recent spills.