Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A

Soil pollution with hexachlorocyclohexane (HCH) has caused serious environmental problems. Here we describe the targeted degradation of all HCH isomers by applying the aerobic bacterium Sphingobium indicum B90A. In particular, we examined possibilities for large-scale cultivation of strain B90A, tested immobilization, storage and inoculation procedures, and determined the survival and HCH-degradation activity of inoculated cells in soil. Optimal growth of strain B90A was achieved in glucose-containing mineral medium and up to 65% culturability could be maintained after 60 days storage at 30°C by mixing cells with sterile dry corncob powder. B90A biomass produced in water supplemented with sugarcane molasses and immobilized on corncob powder retained 15–20% culturability after 30 days storage at 30°C, whereas full culturability was maintained when cells were stored frozen at −20°C. On the contrary, cells stored on corncob degraded γ-HCH faster than those that had been stored frozen, with between 15 and 85% of γ-HCH disappearance in microcosms within 20 h at 30°C. Soil microcosm tests at 25°C confirmed complete mineralization of [¹⁴C]-γ-HCH by corncob-immobilized strain B90A. Experiments conducted in small pits and at an HCH-contaminated agricultural site resulted in between 85 and 95% HCH degradation by strain B90A applied via corncob, depending on the type of HCH isomer and even at residual HCH concentrations. Up to 20% of the inoculated B90A cells survived under field conditions after 8 days and could be traced among other soil microorganisms by a combination of natural antibiotic resistance properties, unique pigmentation and PCR amplification of the linA genes. Neither the addition of corncob nor of corncob immobilized B90A did measurably change the microbial community structure as determined by T-RFLP analysis. Overall, these results indicate that on-site aerobic bioremediation of HCH exploiting the biodegradation activity of S. indicum B90A cells stored on corncob powder is a promising technology.     

Lanthanum biosorption by a Pseudomonas sp.: equilibrium studies and chemical characterization

Lanthanum biosorption by a Pseudomonas sp. was characterized in terms of equilibrium metal loading, model fitting, kinetics, effect of solution pH, lanthanum–bacteria interaction mechanism and recovery of sorbed metal. Lanthanum sorption by the bacterium was rapid and optimum at pH 5.0 with equilibrium metal loading as high as 950 mg g⁻¹ biomass dry wt. Scatchard model and potentiometric titration suggested the presence of at least two types of metal-binding sites, corresponding to a strong and a weak binding affinity. The chemical nature of metal–microbe interaction has been elucidated employing FTIR spectroscopy, energy dispersive X-ray analysis (EDX) and X-ray diffraction analysis (XRD). FTIR spectroscopy and XRD analysis revealed strong involvement of cellular carboxyl and phosphate groups in lanthanum binding by the bacterial biomass. EDX and the elemental analysis of the sorption solution ascertained the binding of lanthanum with the bacterial biomass via displacement of cellular potassium and calcium. Transmission electron microscopy exhibited La accumulation throughout the bacterial cell with some granular deposits in cell periphery and in cytoplasm. XRD confirmed the presence of LaPO₄ crystals onto the bacterial biomass after La accumulation for a long period. A combined ion-exchange–complexation–microprecipitation mechanism could be involved in lanthanum accumulation by the biomass. Almost 98% of biomass-bound La could be recovered using CaCO₃ as the desorbing agent.     

一株鞘氨醇杆菌LF-16的基因组测序与分析

鞘氨醇杆菌属(Sphingobium)是一类具有很强的烷烃、杂环芳香烃降解能力的革兰氏阴性细菌。在NCBI公共数据库报道的95株已测序的鞘氨醇杆菌属基因组中,鲜有和纤维素降解相关。Sphingobium sp.LF-16是在以甘蔗渣为碳源的筛选培养基中筛选得到一株具有纤维素降解能力的菌株。通过对LF-16的基因组测序,得到了一条大小为4.57 Mb,GC含量为64.57%的环状染色体序列,经过基因预测发现该基因组序列共有4340个编码基因,61个转运RNA。使用常用数据库对预测的基因集进行功能注释,获得了4067个编码基因的功能描述信息。通过dbCAN数据库对其编码基因进行分析发现,LF-16共有242个基因的编码产物属于碳水化合物活性酶,其中属于糖苷水解酶家族的有143个,AA家族的辅助蛋白有20个。经分泌组预测,共有488个基因能够分泌到胞外,其中有87个是碳水化合物活性酶。通过与鞘氨醇杆菌属的其他8个菌株的基因组序列进行比较基因组学分析发现LF-16与Sphingobium yanoikuyae SHJ的亲缘关系最近,比除S.yanoikuyae SHJ之外的其他菌株的碳水化合物活性酶的编码基因数量要多20%~30%。     

Localization of HCH catabolic genes (lin genes) in Sphingobium indicum B90A

The locations of hexachlorocyclohexane (HCH) catabolic (lin) genes were investigated in HCH degrading sphingomonad, Sphingobium indicum B90A (that was isolated from India). Southern blot analysis revealed the presence of linA1, linC, linDER and linX (linX1 and linX2) on the plasmid DNA in Sphingobium indicum B90A.     

Short communication: Methylparathion degradation by Pseudomonas sp. A3 immobilized in sodium alginate beads

An organophosphate-degrading soil isolate of Pseudomonas sp. A3, immobilized at 5% (wet wt/v) cell mass in 3% (w/v) sodium alginate beads, detoxified 99% of 1 mm methylparathion in 48 h. The beads were re-usable for five batches, the sixth batch only giving 73% methylparathion removal.     

Maleylacetate reductase of Pseudomonas sp. strain B13: dechlorination of chloromaleylacetates,metabolites in the degradation of chloroaromatic compounds

The maleylacetate reductase of 3-chlorobenzoate-grown cells of Pseudomonas sp. strain B13 has been purified 50-fold. The enzyme converted 2-chloromaleylacetate to 3-oxoadipate with temporary occurrence of maleylacetate; 1 mol of chloride was eliminated during the conversion of 1 mol of 2-chloro- and 2,3-dichloromaleylacetate; 2 mol of NADH were consumed per mol of 2-chloro- and 2,3-dichloromaleylacetate while only 1 mol was necessary to catalyze the conversion of maleylacetate or 2-methylmaleylacetate. The maleylacetate reductase failed to use fumarylacetate as a substrate. The role of the enzyme in the chloroaromatics degradation is discussed.     

High-frequency plant regeneration via adventitious shoot formation from deembryonated cotyledon explants of Sesamum indicum L.

Sesamum indicum L. was used as an important oil crop in the world. An efficient protocol for in vitro plant regeneration via adventitious shoot formation from deembryonated cotyledon explants isolated from mature seeds of sesame is developed. Optimal medium for direct adventitious shoot formation was Murashige and Skoog (MS) medium with 22.2 μM 6-benzylaminopurin (BA) and 5.7 μM indole-3-acetic acid (IAA). Abscisic acid (3.8 μM ABA) and AgNO₃ (29.4 μM) were effective in enhancing the frequency of adventitious shoot formation. Preculture of cotyledon explants on high sucrose concentration (6–9%) for 2 wk and subsequent transfer to 3% sucrose enhanced the frequency of adventitious shoot induction. Root formation from the adventitious shoots was easily achieved on MS medium containing 2.7 μM of α-naphthalene acetic acid (NAA). Regenerated plantlets were acclimatized on sand and peat moss (1:1), showing 95% survival with subsequent flowering and seed set. We established the high-frequency plant regeneration via adventitious shoot formation in S. indicum L.     

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Background

Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results

Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion

The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.     

A novel EDTA-degrading Pseudomonas sp.

A bacterial strain LPM-410 capable of utilizing ethylenediaminetetraacetate (EDTA) as the sole source of energy, carbon, and nitrogen was isolated from sewage sludge and identified as a Pseudomonas sp. on the basis of its phenotypic characteristics. Suspensions of exponential-phase cells degraded EDTA, Mg–, Ca–, Ba–, and Mn–EDTA at constant specific rates ranging from 0.363 to 0.525 mmol EDTA/(g cells h). The more stable chelate, Zn–EDTA, was degraded at a lower rate (0.195 ± 0.030 mmol EDTA/(g cells h)), and here was no degradation of Co–, Cu–, Pb–, and Fe(III)–EDTA.     

Cytogenetic studies on the F1 hybrid Solanum indicum x S. torvum

Summary The F₁ hybrid Solanum indicum x S. torvum could be maintained only under special conditions. Meiosis was highly irregular: about 45% of chromosomes remained as univalents and wherever pairing was observed, it appeared to be loose. A maximum number of three higher chromosome associations other than bivalents, including Y and spoon type associations, indicate extensive chromosome repatterning. Occasional occurrence of twelve bivalents per PMC suggests that, notwithstanding the extreme divergence, the species have retained sufficient ancestral chromosome homoeologies. Chromosome distribution at anaphase-I was highly irregular and precocious division of chromosomes was observed frequently. This hybrid was 100% sterile and the dropping off of immature flower buds was observed.     

Metabolism of benzalphthalide by Pseudomonas sp.

A Pseudomonas sp. degraded benzalphthalide to o-phthalate and benzoate. A tentative pathway for the metabolism of benzalphthalide in this Pseudomonas sp. is proposed on the basis of isolated metabolites, oxygraphic assay and enzymatic studies.     

Organization of three rRNA (rrn) operons from Sphingobium chungbukense DJ77

The nucleotide sequences of all three rRNA operons (rrnA, rrnB, and rrnC) of Sphingobium chungbukense DJ77 were determined. The three rrn operons have the same gene order (16S rRNA-tRNA^Ile-tRNA^Ala-23S rRNA-5S rRNA-tRNA^fMet). The nucleotide sequences were identical over a 5,468 bp region spanning the 16S rRNA gene to the 5S rRNA gene. Variability was observed in the 5S rRNA-tRNA^fMet spacer sequence of rrnB. The tRNA^fMet gene sequences were identical except for two bases (T₅₇₉₄ and A₅₈₇₁ in rrnB, T₅₉₄₂ and A₅₉₅₆ in rrnA, but C₅₉₄₂ and G₅₉₅₆ in rrnC). Comparative sequence analyses of ribosomal RNA operons from DJ77 with those of the class Alphaproteobacteria, to which the genus Sphingobium belongs, reveal close evolutionary relationships with other members of the order Sphingomonadales.     

trans-Stilbene degradation by Arthrobacter sp. SL3 cells

trans-Stilbene degradation was examined by the reaction using resting cells of microorganisms isolated through the enrichment culture using trans-stilbene. The strain SL3, showing the highest trans-stilbene-degrading activity, was identified as Arthrobacter sp. One of the reaction products was identified to be cis,cis-muconic acid. Arthrobacter sp. SL3 cells also transformed benzaldehyde, benzoic acid and catechol into cis,cis-muconic acid, suggesting that one benzene ring of trans-stilbene was converted into cis,cis-muconic acid via benzaldehyde formed by its C_α=C_β bond cleavage.     

Interaction of Fusarium Oxysporum f.sp. Cubense with Pseudomonas Fluorescens Precolonized to Banana Roots

Effect of precolonization of banana cv Neeypovan roots with Pseudomonas fluorescens on infection with Fusarium oxysporum f.sp. cubense was studied. Under in vitro conditions Pseudomonas fluorescens clearly inhibited Fusarium oxysporum f.sp. cubense. Fluorescein isothiocyanate-tagged antibodies raised in a rabbit system for Pseudomonas fluorescens and Fusarium oxysporum f.sp. cubense separately were used to study the spread of both organisms in banana root. It was observed that precolonization with Pseudomonas fluorescens could reduce Fusarium oxysporum f.sp. cubense colonization by 72%, and also correlated with a number of structural changes in the cortical cells, mainly with densely stained amorphous material and polymorphic wall thickenings as revealed by light and electron microscopic studies. Massive depositions of unusual structures at sites of fungal entry was also noticed, which clearly indicated that bacterized root cells were signalled to mobilize a number of defence structures for preventing the spread of pathogen in the tissue. This revised version was published online in July 2006 with corrections to the Cover Date.     

Growth of a manganese oxidizing Pseudomonas sp. in continuous culture

Strain S-36, a marine Pseudomonas sp., was grown under manganese limitation in continuous culture. At dilution rates below a maximal growth rate of 0.066 h^-1, the rate at which the organism fixed CO₂ into macromolecules was equal to the cell carbon production rate. In addition, the total amount of cell carbon or CO₂ fixed at steady-state was in proportion to the amount of energy available from the oxidation of Mn²⁺ in the medium. These data suggest that the organism can grow by obtaining the energy for CO₂ fixation from manganese oxidation.     

New metabolic pathway for o-cresol degradation by Pseudomonas sp. CP4 as evidenced by 1H NMR spectroscopic studies

Degradation intermediates of o-, m- and p-cresols extracted from resting cells of Pseudomonas sp. CP4, a potent cresol- and phenol-degrading laboratory isolate, were analysed by using ¹H NMR spectroscopy at 270 MHz. Ortho-, meta- and para-cresols were found to be degraded to 2-methyl-4-oxalocrotonate. 3-Methylcatechol from o-cresol was degraded further to 2-ketohex-cis-4-enoate, 4-methylcatechol from m- and p-cresol was degraded to 2-ketohex-cis-4-enoate. Also 2-ketopent-4-enoate was found to be formed from p-cresol. Formation of 2-methyl-4-oxalocrotonate was envisaged as taking place from 5-hydroxy-2-methylmuconic semialdehyde, the ring-cleavage product of 4-methylresorcinol, a possible product by hydroxylation of o-cresol along with 3-methylcatechol. This is a deviation from the hitherto known pathways of o-cresol degradation. Based on these observations, pathways for the degradation of all three isomers of cresol are proposed.     

Pseudomonas aeruginosa protease IV enzyme assays and comparison to other Pseudomonas proteases

Pseudomonas aeruginosa secretes multiple proteases that have been implicated as virulence factors and the detection of each specific enzyme can be difficult to determine. Unlike the three Pseudomonas enzymes that have been well characterized (elastase A, elastase B, and alkaline protease), the activity of protease IV in multiple assays has yet to be described. This study defines new assays for Pseudomonas proteases and compares protease IV activity to the activities of elastase A, elastase B, and alkaline protease. Six in vitro assays were studied: zymography, elastin congo red assay, staphylolytic assay, colorimetric peptide assay, solid-phase colorimetric peptide assay, and poly-l-lysine degradation. Casein zymography distinguished protease IV from elastase B and alkaline protease, and gelatin zymography differentiated all four proteases. The elastin congo red assay detected mainly elastase B while the staphylolytic assay was specific for elastase A. Protease IV activity was assayed specifically by the colorimetric assay and two new assays, the solid-phase colorimetric assay and degradation of poly-L-lysine in the presence of EDTA. Alkaline protease could be specifically assayed by poly-L-lysine degradation in the presence of N-alpha-p-tosyl-L-lysine chloromethyl ketone. The results identified three specific assays for protease IV, a new assay specific for alkaline protease, and showed that protease IV has a distinct enzymatic specificity relative to the three other Pseudomonas proteases.     

Spirosymplokos deltaeiberi nov. gen., nov. sp.: variable-diameter composite spirochete from microbial mats

Large (up to 100 m long), loosely coiled, free-living spirochetes with variable diameters (from 0.4 to 3 m in the same cell) were seen at least 40 times between August 1990 and January 1993. These spirochetes were observed in mud water and enrichment media from highly specific habitats in intertidal evaporite flats at three disjunct localities, one in Spain and two in Mexico. All three are sites of commerical saltworks. Associated with Microcoleus chthonoplastes, the large spirochetes from Spain display phototaxis and a composite organization. Shorter and smaller-diameter spirochetes are seen inside both healthy and spent periplasm of larger ones. Small spirochetes attached to large ones have been observed live. From two to twelve spirochete protoplasmic cylinders were seen inside a single common outer membrane. A distinctive granulated cytoplasm in which the granules are of similar diameter (20–32 nm) to that of the flagella (26 nm) was present. Granule diameters were measured in thin section and in negatively-stained whole-mount preparations. Based on their ultrastructure, large size, variable diameter, number of flagella (3 to 6), and phototactic behavior these unique spirochetes are formally named Spirosymplokos deltaeiberi. Under anoxic (or low oxygen) conditions they formed blooms in mixed culture in media selective for spirochetes. Cellobiose was the major carbon source in 80% seawater, the antibiotic rifampicin was added, mat from the original field site was present and tubes were incubated in the light at from 18–31 °C. Within 1–2 weeks populations of the large spirochete developed at 25 °C but they could not be transferred to fresh medium.     

Degradation of carbazole and its derivatives by a Pseudomonas sp.

Carbazole, carbazoles with monomethyl or dimethyls substituted on different positions (C₁-carbazoles or C₂-carbazoles), and benzocarbazoles, as toxic and mutagenic components of petroleum and creosote contamination, were biodegradable by an isolated bacterial strain Pseudomonas sp. XLDN4-9. C₁-carbazoles were degraded in preference to carbazole and C₂-carbazoles. The biodegradation of C₁-carbazoles or C₂-carbazoles was influenced by the positions of methyl substitutions. Among C₁-carbazole isomers, 1-methyl carbazole was the most susceptible. C₂-carbazole isomers with substitutions on the same benzo-nucleus were more susceptible at a concentration of less than 3.4 μg g⁻¹ petroleum, especially when harboring one substitution on position 1. In particular, 1,5-dimethyl carbazole was the most recalcitrant dimethyl isomer.