Diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater

Chlorophenol-degrading bacteria from a long-term polluted groundwater aquifer were characterized. All isolates degraded 2,4,6-trichlorophenol and 2,3,4,6-tetrachlorophenol at concentrations detected in the contaminated groundwater (< 10 mg l^–1). Pentachlorophenol was degraded by three isolates when present alone. In two gram-positive isolates, 2,3,4,6-tetrachlorophenol was required as an inducer for the degradation of pentachlorophenol. The gram-positive isolates were sensitive to pentachlorophenol, with an IC₅₀ value of 5 mg/l. Isolates belonging to the Cytophaga/Flexibacter/Bacteroides phylum had IC₅₀ values of 25 and 63 mg/l. Isolates belonging to α-, β- and γ-Proteobacteria generally tolerated the highest pentachlorophenol concentrations (> 100 mg/l). Polychlorophenol-degrading capacity was found in strains of Nocardioides, Pseudomonas, Ralstonia, Flavobacterium, and Caulobacter previously not known to degrade polychlorophenols. In addition, six polychlorophenol-degrading sphingomonads were found. Received: 27 September 1998 / Accepted: 21 December 1998     

Different Modes of Diaminopimelate Synthesis and Their Role in Cell Wall Integrity: a Study with Corynebacterium glutamicum

In eubacteria, there are three slightly different pathways for the synthesis of m-diaminopimelate (m-DAP), which is one of the key linking units of peptidoglycan. Surprisingly, for unknown reasons, some bacteria use two of these pathways together. An example is Corynebacterium glutamicum, which uses both the succinylase and dehydrogenase pathways for m-DAP synthesis. In this study, we clone dapD and prove by enzyme experiments that this gene encodes the succinylase (M_r = 24082), initiating the succinylase pathway of m-DAP synthesis. By using gene-directed mutation, dapD, as well as dapE encoding the desuccinylase, was inactivated, thereby forcing C. glutamicum to use only the dehydrogenase pathway of m-DAP synthesis. The mutants are unable to grow on organic nitrogen sources. When supplied with low ammonium concentrations but excess carbon, their morphology is radically altered and they are less resistant to mechanical stress than the wild type. Since the succinylase has a high affinity toward its substrate and uses glutamate as the nitrogen donor, while the dehydrogenase has a low affinity and incorporates ammonium directly, the m-DAP synthesis is another example of twin activities present in bacteria for access to important metabolites such as the well-known twin activities for the synthesis of glutamate or for the uptake of potassium.     

Functional and composition differences between mitochondrial complex II in Arabidopsis and rice are correlated with the complex genetic history of the enzyme

Complex II plays a central role in mitochondrial metabolism as a component of both the electron transport chain and the tricarboxylic acid cycle. However, the composition and function of the plant enzyme has been elusive and differs from the well-characterised enzymes in mammals and bacteria. Herewith, we demonstrate that mitochondrial Complex II from Arabidopsis and rice differ significantly in several aspects: (1) Stability—Rice complex II in contrast to Arabidopsis is not stable when resolved by native electrophoresis and activity staining. (2) Composition—Arabidopsis complex II contains 8 subunits, only 7 of which have homologs in the rice genome. SDH 1 and 2 subunits display high levels of amino acid identity between two species, while the remainder of the subunits are not well conserved at a sequence level, indicating significant divergence. (3) Gene expression—the pairs of orthologous SDH1 and SDH2 subunits were universally expressed in both Arabidopsis and rice. The very divergent genes for SDH3 and SDH4 were co-expressed in both species, consistent with their functional co-ordination to form the membrane anchor. The plant-specific SDH5, 6 and 7 subunits with unknown functions appeared to be differentially expressed in both species. (4) Biochemical regulation -succinate-dependent O₂ consumption and SDH activity of isolated Arabidopsis mitochondria were substantially stimulated by ATP, but a much more minor effect of ATP was observed for the rice enzyme. The ATP activation of succinate-dependent reduction of DCPIP in frozen-thawed and digitonin-solubilised mitochondrial samples, and with or without the uncoupler CCCP, indicate that the differential ATP effect on SDH is not via the protonmotive force but likely due to an allosteric effect on the plant SDH enzyme itself, in contrast to the enzyme in other organisms.     

Effects of different mineral supplements on fertilization of phenol-contaminated soils by Corynebacterium glutamicum

This study focused on the effects of different mineral supplements on the ability of Corynebacterium glutamicum to degrade phenol in contaminated soil and convert the phenol into useful amino acids. Three types of minerals including FeSO₄, MgSO₄, and MnSO₄ were added at several concentrations to C. glutamicum culture media containing 1% yeast extract prior to treating the soil samples with 4.24 mM phenol. The reactor was incubated at 30°C and 150 rpm for 3 days, and the treated soil was sampled daily and analyzed using gas chromatography for residual phenol and the amino acids produced. Additionally, a plant toxicity assay was employed to examine the fertilization of the phenol-contaminated soil after C. glutamicum treatment supplemented with the three minerals. Our results suggested that among various tested concentrations, 72 μM of iron showed a significant effect on the utilization of phenol by C. glutamicum for conversion to amino acids, therefore enhancing fertilization of the phenol-contaminated soil.     

Key enzymes of the protocatechuate branch of the β-ketoadipate pathway for aromatic degradation inCorynebacterium glutamicum

Although the protocatechuate branch of the β-ketoadipate pathway in Gram⁻ bacteria has been well studied, this branch is less understood in Gram⁺ bacteria. In this study,Corynebacterium glutamicum was cultivated with protocatechuate,p-cresol, vanillate and 4-hydroxybenzoate as sole carbon and energy sources for growth. Enzymatic assays indicated that growing cells on these aromatic compounds exhibited protocatechuate 3,4-dioxygenase activities. Data-mining of the genome of this bacterium revealed that the genetic locusncg12314-ncg12315 encoded a putative protocatechuate 3,4-dioxygenase. The genes,ncg12314 andncg12315, were amplified by PCR technique and were cloned into plasmid (pET21aP34D). RecombinantEscherichia coli strain harboring this plasmid actively expressed protocatechuate 3,4-dioxygenase activity. Further, when this locus was disrupted inC. glutamicum, the ability to degrade and assimilate protocatechuate,p-cresol, vanillate or 4-hydroxybenzoate was lost and protocatechuate 3,4-dioxygenase activity was disappeared. The ability to grow with these aromatic compounds and protocatechuate 3,4-dioxygenase activity ofC. glutamicum mutant could be restored by gene complementation. Thus, it is clear that the key enzyme for ring-cleavage, protocatechuate 3,4-dioxygenase, was encoded byncg12314 andncg12315. The additional genes involved in the protocatechuate branch of the β-ketoadipate pathway were identified by mining the genome data publically available in the Gen Bank. The functional identification of genes and their unique organization inC. glutamicum provided new insight into the genetic diversity of aromatic compound degradation.     

Long-chain acylhomoserine lactones increase the anoxic ammonium oxidation rate in an OLAND biofilm

The oxygen-limited autotrophic nitrification/denitrification (OLAND) process comprises one-stage partial nitritation and anammox, catalyzed by aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB), respectively. The goal of this study was to investigate whether quorum sensing influences anoxic ammonium oxidation in an OLAND biofilm, with AnAOB colonizing 13% of the biofilm, as determined with fluorescent in situ hybridization (FISH). At high biomass concentrations, the specific anoxic ammonium oxidation rate of the OLAND biofilm significantly increased with a factor of 1.5 ± 0.2 compared to low biomass concentrations. Supernatant obtained from the biofilm showed no ammonium-oxidizing activity on itself, but its addition to low OLAND biomass concentrations resulted in a significant activity increase of the biomass. In the biofilm supernatant, the presence of long-chain acylhomoserine lactones (AHLs) was shown using the reporter strain Chromobacterium violaceum CV026, and one specific AHL, N-dodecanoyl homoserine lactone (C₁₂-HSL), was identified via LC-MS/MS. Furthermore, C₁₂-HSL was detected in an AnAOB-enriched community, but not in an AerAOB-enriched community. Addition of C₁₂-HSL to low OLAND biomass concentrations resulted in a significantly higher ammonium oxidation rate (p < 0.05). To our knowledge, this is the first report demonstrating that AHLs enhance the anoxic ammonium oxidation process. Future work should confirm which species are responsible for the in situ production of C₁₂-HSL in AnAOB-based applications.     

不同氮源及其浓度对标志链带藻合成淀粉和油脂的影响北大核心CSCD

【目的】以标志链带藻(Desmodesmus insignis)为实验材料,研究不同氮源及其浓度对该藻生长、总脂和淀粉(碳水化合物)含量的影响,为该藻在生物能源方面的应用提供一定的理论依据。【方法】以硝酸钠、碳酸氢铵或尿素为氮源,5个氮浓度(3、6、9、12和18 mmol/L)的BG-11培养基培养标志链带藻,采用干重法测定生物质浓度、重量法测定总脂、苯酚-硫酸法测定、总碳水化合物和淀粉的含量。【结果】标志链带藻在3种氮源下均能很好的生长。最高油脂含量出现在3 mmol/L硝酸钠实验组,达到32.61%(d.w)。当18 mmol/L碳酸氢铵作为氮源时,总碳水化合物与淀粉的含量以及产率都达到最高,分别为56.54%(d.w)和55.33%(d.w)、0.24和0.23 g/(L·d)。以尿素为氮源时,其生物质浓度和各组分含量与其它氮源实验组差别不大,均有利于该藻的生长及各生化组分含量的积累。【结论】以该藻种生产生物能源的成本等综合考虑,以18 mmol/L碳酸氢铵和尿素为氮源培养标志链带藻最优。     

Three newSalmonella types (S. Bilthoven,S. wassenaar andS. bonaire

Summary Two newSalmonella types,S. bilthoven, 47ac: a:—andS. wassenaar, 50; gp—were isolated from reptiles in the Netherlands. A newSalmonella type,S. bonaire 50; z₄z₃₂:— was isolated from a cow on the Island Bonaire.     

Effects of Rhamnolipids from Pseudomonas aeruginosa DS10-129 on Luminescent Bacteria: Toxicity and Modulation of Cadmium Bioavailability

In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri and recombinant bioluminescent Pseudomonas fluorescens, P. aeruginosa, Escherichia coli, and Gram-positive Bacillus subtilis were used as model organisms. Rhamnolipids reduced the bioluminescence of these bacteria in less than a second of exposure even in relatively low concentrations (30-min EC₅₀ 45–167 mg l⁻¹). Toxicity of Cd to Gram-negative bacteria (30-min EC₅₀ values 0.16 mg l⁻¹ for E. coli, 0.96 mg l⁻¹ for P. fluorescens, and 4.4 mg l⁻¹ for V. fischeri) was remarkably (up to 10-fold) reduced in the presence of 50 mg l⁻¹ rhamnolipids. Interestingly, the toxicity of Cd to Gram-positive B. subtilis (30-min EC₅₀ value 0.49 mg l⁻¹) was not affected by rhamnolipids. Rhamnolipids had an effect on desorption of Cd from soil: 40 mg l⁻¹ rhamnolipids increased the water-extracted fraction of Cd twice compared with untreated control. However, this additionally desorbed fraction of Cd remained bound with rhamnolipids and was not available to bacteria. Hence, in carefully chosen concentrations (still effectively complexing heavy metals but not yet toxic to soil bacteria), rhamnolipids could be applied in remediation of polluted areas.     

Antisettlement and Narcotic Action of Analogues of Diterpene Marine Natural Product Antifoulants from Octocorals

Prevoius studies have determined that the octocorals Renilla reniformis and Leptogorgia virgulata contain diterpenes that are potent inhibitors of barnacle settlement. These antifoulants—the renillafoulins and pukalide—are, however, comparatively complex and thus are not amenable to commercial exploitation. The present study examined 19 analogues, based on the functional groups of lactone and furan rings in the parent molecules, for antisettlement activity and toxicity. The latter parameters are presented as EC₅₀ values for inhibition of cypris settlement and naupliar swimming, respectively. Assays of a subset of the analogues indicated that they were active in solution rather than when bound to a surface and that at relatively high concentrations they had a narcotic action. The mechanism whereby some of the analogues were able to inhibit settlement at nontoxic concentrations has yet to be explained but suggests that there is merit in the present approach to antifoulant development. Received April 1, 1998; accepted February 4, 1999.     

Effect of ammonia on sucrose synthase in pea roots

The effects of ammonium on activity of sucrose synthase (SS) in the roots of pea (Pisum sativum L.) plants were studied. On the medium containing 14.2 mM (NH₄)₂SO₄, SS activity increased by 20–200% for 10–20 days of plant growth as compared with the roots of plants growing without nitrogen. Illuminance affected the degree of effects. Under natural illumination, ammonium affected SS activity not only in sunny days (up to 25 klx) but also in cloudy days (3–6 klx) but to a lower degree. Under stable low light (2.5 klx), ammonium did not affect SS activity. In the in vitro experiments, at (NH₄)₂SO₄ concentrations from 0 to 1 mM, SS activity was suppressed (up to 10%), whereas 1–37.5 mM (NH₄)₂SO₄, it was increased (up to 50%).     

Positive effect of shredders on microbial biomass and decomposition in stream microcosms

1. Animals play a major role in nutrient cycling via excretory processes. Although the positive indirect effects of grazers on periphytic algae are well understood, little is known about top‐down effects on decomposers of shredders living on leaf litter. 2. Nutrient cycling by shredders in oligotrophic forest streams may be important for the microbial‐detritus compartment at very small spatial scales (i.e. within the leaf packs in which shredders feed). We hypothesised that insect excretion may cause local nutrient enrichment, so that microorganism growth on leaves is stimulated. 3. We first tested the effect of increasing concentration of ammonium (+10, +20 and +40 μg NH₄⁺ L^?1) on fungal and bacterial biomass on leaf litter in a laboratory experiment. Then we performed two experiments to test the effect of the presence and feeding activity of shredder larvae. We used two species belonging to the trichopteran family Sericostomatidae: the Palaearctic Sericostoma vittatum and the Neotropical Myothrichia murina, to test the effect of these shredders on fungal and bacterial biomass and decomposition on leaves of Quercus robur and Nothofagus pumilio, respectively. All experiments were run in water with low ammonium concentrations (2.4 ± 0.34 to 14.47 ± 0.95 μg NH₄⁺ L^?1). 4. After 5 days of incubation, NH₄ concentrations were reduced to near‐ambient streamwater concentrations in all treatments with leaves. Fungal biomass was positively affected by increased ammonium concentration. On the other hand, bacteria abundance was similar in all treatments, both in terms of abundance (bacteria cells mg^?1 leaf DW) and biomass. However, there was a tendency towards larger mean cell size in treatments with 20 μg NH₄ L^?1. 5. In the experiment with S. vittatum, fungal biomass in the treatment with insects was more than twice that in the control after 15 days. Bacteria were not detected in treatments with insects, where hyphae were abundant, but they were abundant in treatments without larvae. In the decomposition experiment run with M. murina, leaf‐mass loss was significantly higher in treatments with larvae than in controls. 6. Our hypothesis of a positive effect of shredders on fungal biomass and decomposition was demonstrated. Insect excretion caused ammonium concentration to increase in the microcosms, contributing to microbial N uptake in leaf substrata, which resulted in structural and functional changes in community attributes. The positive effect of detritivores on microbes has been mostly neglected in stream nutrient‐cycling models; our findings suggest that this phenomenon may be of greater importance than expected in stream nutrient budgets.     

Soybean [Glycine max (L.) merrill] embryogenic cultures: The role of sucrose and total nitrogen content on proliferation

Summary To improve proliferation of soybean cultures in liquid medium, the effects of sucrose; total inorganic nitrogen; content of No₃ ⁻, NH₄ ⁺, Ca²⁺, PO₄ ³⁻, K⁺; NH₄ ⁺/NO₃ ⁻ ratio; and medium osmotic pressure were studied using cv. Jack. Sucrose concentration, osmotic pressure, total nitrogen content, and ammonium to nitrate ratio were found to be the major factors controlling proliferation of soybean embryogenic cultures. Growth decreased linearly as sucrose concentration increased from 29.7 mM to 175.3 mM. A sucrose concentration of 29.2 mM, a nitrogen content of 34.9 mM, at 1 to 4 ammonium to nitrate ratio were found to be optimal for the fastest proliferation of soybean embryogenic cultures. There was no significant effect on proliferation of cultures when concentrations of NH₄ ⁺, Ca²⁺, PO₄ ³⁻, and K⁺ were tested in the range of 3.50 to 10.50, 1.02 to 3.06, 0.68 to 2.04, and 22.30 to 36.70 mM, respectively. The relative proliferation of embryogenic cultures of four soybean genotypes was evaluated in Finer and Nagasawa medium and in the new medium formulation. Despite genotype-specific differences in growth, the genotypes tested showed a biomass increase in the new formulation equal to 278, 269, 170, and 251% for Chapman, F138, Jack, and Williams 82, respectively, relative to their growth on standard FN medium. Due to its lowered sucrose and nitrogen content, we are referring to the new medium as FN Lite.     

Induction of only limited elongation instead of filamentation by inhibition of cell division in Corynebacterium glutamicum

In order to characterize the cell-division mechanism of coryneform bacteria, we tried to isolate cell-division mutants from Corynebacterium glutamicum after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis, such as Escherichia coli fts mutants, which form long filaments at the restrictive temperatures. At the non-permissive temperature, most of the mutants formed club-shaped or dumbbell-shaped, elongated rod cells, but no filament formers were isolated. Then we examined the effects of cell division inhibitors on this organism. Cephalexin and sparfloxacin, which are the inhibitors of septation and DNA synthesis respectively, and are known to cause cell filamentation in E. coli, did not cause filamentation in C. glutamicum but induced morphological changes that were similar to those observed with the temperature-sensitive ts mutants of C.␣glutamicum. These results suggest that C. glutamicum has a unique regulation mechanism, that is, the inhibition of cell division leads to cessation of cell elongation. Received: 5 February 1998 / Received revision: 6 April 1998 / Accepted: 27 April 1998     

Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures

We describe a new device with parallel optical measurement of dissolved oxygen (DO) and pH in up to nine shake flasks applicable in any conventional shaking incubator. Measurement ranges are 0–500% of air saturation for oxygen and 5.5–8.5 for pH. It was used to characterize growth profiles of different l-lysine producing strains of Corynebacterium glutamicum, of Saccharomyces cerevisiae and of Escherichia coli. Cultures in unbaffled flasks were highly reproducible. Oxygen limitation was indicated online which is particularly important when cultivating fast growing cells as E. coli. C. glutamicum strains showed distinct characteristic patterns of DO and pH indicating biological events. During the cultivation of S. cerevisiae on glucose, fructose and galactose, oxygen uptake rate was determined using the predetermined value of k _L a. pH measurement was used to determine the minimum buffer requirement for a culture of C. glutamicum.     

双功能尿苷酰转移/去除酶GlnD在谷氨酸棒杆菌JNR中的功能

【目的】通过改造谷氨酸棒杆菌JNR中双功能尿苷酰转移/去除酶GlnD,减弱尿苷酰去除酶的活性,增强NH_4~+的转运和利用,提高L-精氨酸的合成。【方法】本文对来源于谷氨酸棒杆菌的突变菌株JNR中的双功能尿苷酰转移/去除酶GlnD进行整合突变,采用同源重组的方法将H_(414)和D_(415)位点突变为两个丙氨酸AA,在此菌株的基础上过量表达PII蛋白GlnK,并对其进行尿苷酰化研究,离子色谱检测摇瓶发酵过程中NH4+的浓度,并对最终的改造菌株进行连续流加发酵分析。【结果】该双功能尿苷酰转移/去除酶在谷氨酸棒杆菌中成功进行整合突变,有效减弱了尿苷酰去除酶的活性;同时过表达PII蛋白GlnK,其酰基化程度明显增强。摇瓶发酵结果表明菌株L4消耗NH_4~+增加,L-精氨酸产量为36.2±1.2 g/L,比对照菌株L3高出22.7%。5-L发酵罐实验结果显示改造菌株L4的L-精氨酸的产量为52.2 g/L,较野生型菌株L0提高了25.3%。【结论】谷氨酸棒杆菌合成L-精氨酸的过程中氮源是必不可少的。减弱GlnD尿苷酰去除酶的活性后,胞内尿苷酰化的GlnK-UMP增加,GlnK-UMP与氮转录调控因子AmtR结合,转运至胞内的NH_4~+浓度提高,促使L-精氨酸产量显著提高。     

Cell envelope fluidity modification for an effective glutamate excretion in <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis> 2262

1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) was used to assess the cell envelope fluidity of Corynebacterium glutamicum 2262 during a temperature-triggered glutamate producing process. Because the fluorescence lifetime of TMA-DPH was shown to be constant all over the process, fluorescence anisotropy can be considered as a good index of cell envelope fluidity. When the temperature of the fed-batch culture was increased from 33 to 39°C to induce glutamate excretion, the fluorescence anisotropy values decreased from 0.212 ± 0.002 to 0.186 ± 0.002 (corresponding to an increase in the cell fluidity), while the specific glutamate production rate reached its maximal value. The increase in fluidity of the C. glutamicum cell envelope was not due to a physical effect related to the temperature elevation, but rather to an alteration of the composition of the cell envelope. Using a mutant devoid of corynomycolates, significant differences in fluorescence anisotropy values were obtained compared to the wild-type strain, suggesting that TMA-DPH is mainly anchored into the corynomycomembrane. Differences in fluorescence anisotropy were also observed when the bacteria were cultivated at 33, 36, 38, and 39°C in batch cultures, and a linear relationship was obtained between the maximum specific glutamate production rate and the measured fluidity. When using the glutamate non-producing variant of C. glutamicum 2262, the fluorescence anisotropy remained constant at 0.207 ± 0.003 whatever the applied temperature shift. This suggests that the fluidity of the Corynebacteria mycomembrane plays an important role in glutamate excretion during the temperature-triggered process.     

Medicinal herb extracts inhibit growth of<Emphasis Type="Italic">Rhabditis elongate</Emphasis> (Nematoda:<Emphasis Type="Italic">Rhabditidae</Emphasis>)

We tested the influence of extracts from three medicinal herbs —Salvia miltiorrhiza, Schizandra chinensis, andEugenia caryophyllata — on activity of the nematodeRhabditis elongate. Treatment with f.caryophyllata was most useful, causing the greatest decrease in populations and mobility, but did not have any detrimental effect on the initial growth of the host microorganism,Escherichia coli. For example, when 0.5 g/L of the extract was added to an inoculated liquid culture, we counted 710 nematodes/mL, with a multiplication rate 5 times greater than the initial population. This was in contrast to the control sample, which had a count of 1100 nematodes/mL and a growth ratio of 11. For our field test, nematode mobility in the presence of the extract also decreased, to 6.8 mm/day, compared with 20 mm/day for the control. Likewise, when 1.0 g/L of the extract was added to the soil, the total number of nematodes was reduced to only 30- to 40% of the control population.