The catabolism and heterotrophic nitrification of the siderophore deferrioxamine B

Summary Three bacteria, two of which were previously noted as active heterotrophic nitrifiers, were examined for their ability to grow and nitrify with the siderophore deferrioxamine B as the carbon source.Pseudomonas aureofaciens displayed limited growth and nitrification while a heterotrophic nitrifyingAlcaligenes sp. was without action concerning its metabolism of deferrioxamine B. The third bacterium, a unique Gram-negative soil isolate, was unable to nitrify deferrioxamine B but grew well when the siderophore was employed as the sole C source. The Gram-negative bacterium removed deferrioxamine B from the medium and left only residual amounts of the compound in solution at the termination of its growth. The organism was without action when the ferrated analogue of deferrioxamine B, ferrioxamine B, sereved as either the C source for growth, for metabolism by resting cells, or as the substrate for cell-free extracts. Deferrioxamine B, by contrast, was rapidly metabolized by resting cells. Cell-free extracts of the bacterium synthesized a monohydroxamate(s) when deferrioxamine B was the substrate. The catabolism of deferrioxamine B, which is synthesized by soil microbes, suggests that soil microflora have the ability to return deferrioxamine B, and perhaps other, siderophores to the C cycle.Abbreviations DFB deferrioxamine B; - FB ferrioxamine B - PhMeSO₂F phenylmethylsulfonyl fluoride     

A spectrophotometric assay for the degradation of the siderophore deferrioxamine B

A spectrophotometric assay using ferric perchlorate in a perchloric acid solution has been developed to monitor the degradation of the trihydroxamate siderophore deferrioxamine B to monohydroxamates. Using the ferric perchlorate solution and employing various concentrations of acetohydroxamic acid (as the model monohydroxamic acid) while maintaining a constant amount of deferrioxamine B resulted in the shifting of the absorption maximum from that of ferrioxamine B to longer wavelengths and toward that of a pure ferri-acetomonohydroxamic acid solution. A similar result was noted when a cell-free extract, from a bacterium capable of using deferrioxamine B as its sole carbon source, was given the siderophore in a phosphate buffer and aliquots of the enzyme-deferrioxamine B solution were removed for analysis. The assay may thus be used to monitor the formation of the monohydroxamic acid degradation products of the siderophore by the enzyme(s) in the cell-free extract.     

Degradation pathway and generation of monohydroxamic acids from the trihydroxamate siderophore deferrioxamine B

Siderophores are avid ferric ion-chelating molecules that sequester the metal for microbes. Microbes elicit siderophores in numerous and different environments, but the means by which these molecules reenter the carbon and nitrogen cycles is poorly understood. The metabolism of the trihydroxamic acid siderophore deferrioxamine B by a Mesorhizobium loti isolated from soil was investigated. Specifically, the pathway by which the compound is cleaved into its constituent monohydroxamates was examined. High-performance liquid chromatography and mass-spectroscopy analyses demonstrated that M. loti enzyme preparations degraded deferrioxamine B, yielding a mass-to-charge (m/z) 361 dihydroxamic acid intermediate and an m/z 219 monohydroxamate. The dihydroxamic acid was further degraded to yield a second molecule of the m/z 219 monohydroxamate as well as an m/z 161 monohydroxamate. These studies indicate that the dissimilation of deferrioxamine B by M. loti proceeds by a specific, achiral degradation and likely represents the reversal by which hydroxamate siderophores are thought to be synthesized.     

Effects of deferrioxamine on iron-catalyzed lipid peroxidation.

The kinetics of iron binding by deferrioxamine B mesylate and the ramifications of this process upon iron-catalyzed lipid peroxidation were assessed. The relative rates of Fe(III) binding by deferrioxamine varied for the chelators tested as follows: ADP greater than AMP greater than citrate greater than histidine greater than EDTA. The addition of a fivefold molar excess of deferrioxamine to that of Fe(III) did not result in complete binding (within 10 min) for any of the Fe(III) chelates tested except ADP:Fe(III). The rates of Fe(III) binding by deferrioxamine were greater at lower pH and when the competing chelator concentration was high in relationship to iron. The relatively slow binding of Fe(III) by deferrioxamine also affected lipid peroxidation, an iron-dependent process. The addition of deferrioxamine to an ascorbate- and ADP:Fe(III)-dependent lipid peroxidation system resulted in a time-dependent inhibition or stimulation of malondialdehyde formation (i.e., lipid peroxidation), depending on the ratio of deferrioxamine to iron. Converse to Fe(III), the rates of Fe(II) binding by deferrioxamine from the chelators tested above were rapid and complete (within 1 min), and resulted in the oxidation of Fe(II) to Fe(III). Lipid peroxidation dependent on Fe(II) autoxidation was stimulated by the addition of deferrioxamine. Malondialdehyde formation in this system was inhibited by the addition of catalase, and a similar extent of lipid peroxidation was achieved by substituting hydrogen peroxide for deferrioxamine. Collectively, these results suggest that the kinetics of Fe(III) binding by deferrioxamine is a slow, variable process, whereas Fe(II) binding is considerably faster. The binding of either valence of iron by deferrioxamine may result in variable effects on iron-catalyzed processes, such as lipid peroxidation, either via slow binding of Fe(III) or the rapid binding of Fe(II) with concomitant Fe(II) oxidation.     

Degradation Pathway and Generation of Monohydroxamic Acids from the Trihydroxamate Siderophore Deferrioxamine B

Siderophores are avid ferric ion-chelating molecules that sequester the metal for microbes. Microbes elicit siderophores in numerous and different environments, but the means by which these molecules reenter the carbon and nitrogen cycles is poorly understood. The metabolism of the trihydroxamic acid siderophore deferrioxamine B by a Mesorhizobium loti isolated from soil was investigated. Specifically, the pathway by which the compound is cleaved into its constituent monohydroxamates was examined. High-performance liquid chromatography and mass-spectroscopy analyses demonstrated that M. loti enzyme preparations degraded deferrioxamine B, yielding a mass-to-charge (m/z) 361 dihydroxamic acid intermediate and an m/z 219 monohydroxamate. The dihydroxamic acid was further degraded to yield a second molecule of the m/z 219 monohydroxamate as well as an m/z 161 monohydroxamate. These studies indicate that the dissimilation of deferrioxamine B by M. loti proceeds by a specific, achiral degradation and likely represents the reversal by which hydroxamate siderophores are thought to be synthesized.     

The nutritional selectivity of a siderophore-catabolizing bacterium

The ability of a siderophore-catabolizing bacterium to assimilate ferric ion was examined. While the bacterium utilizes the siderophore deferrioxamine B (DFB) as a carbon source, it was incapable of using the ferricion analogue (ferrioxamine B) as an iron source. It did, however, assimilate the ferric ion of the chelator ferric nitrilotriacetic acid and of the siderophore ferrirhodotorulic acid (ferriRA). Neither ferriRA nor its deferrated analog (RA), however, were capable of functioning as carbon sources for the bacterium. The microbe thus employs a nutritional selectivity with respect to these two siderophores. That is, it does not use the siderophore it employs as a carbon source (DFB) as an iron source nor does the siderophore utilized as an iron source, i.e. ferriRA, nor its deferrated analog (RA), serve as carbon sources for the organism.This paper is dedicated to the memory of Professor Thomas Emery. Professor Emery was instrumental in giving support and advice at a time when such mentorship greatly aided the corresponding author in developing a program concerning the catabolism of siderophores by microbes.     

降解菌HN36对二氯喹啉酸胁迫下烟草茎尖和叶片超微结构的影响

利用降解菌HN36降解土壤中的二氯喹啉酸及修复土壤的生态环境, 为稻田植烟地区烟叶安全生产提供技术和理论依据。采用盆栽试验, 将二氯喹啉酸与降解菌HN36配成一定量的溶液, 均匀喷洒到过筛的干土中, 将5叶期烟苗移栽到处理的塑料盆土中。当烟苗长到8叶期时分别取茎尖﹑顶叶和中部叶进行处理, 在电镜下观察细胞超微结构变化, 利用高效液相色谱仪检测土壤中二氯喹啉酸降解的动态。烟株细胞超微结构变化的程度有差异, 表现为受害烟株>修复烟株>健康烟株; 烟株的茎尖和顶叶细胞伤害最严重, 中部叶片细胞伤害较轻。研究结果还显示, 在含二氯喹啉酸的土壤中, 加入降解菌HN36能加速二氯喹啉酸降解, 改善土壤健康质量, 烟株细胞超微结构及烟叶品质明显得到修复。     

Degradation of Trichloroethylene by <Emphasis Type="Italic">Bacillus</Emphasis> sp.: Isolation Strategy,Strain Characteristics,and Cell Immobilization

A novel isolate of a bacterium, capable of degrading trichloroethylene (TCE) and growing on this as the sole carbon source is reported. The test strain was isolated by an enrichment technique with trichloroethylene as the substrate. The isolated strain belongs to the genus Bacillus. The practical utility of cleaning up oil spillage by bioremediation could be extended to this bacterium to degrade the environmental pollutant, which is used in metal degreasing in industries. Cells of the novel bacterium immobilized on calcium alginate were found to have better trichloroethylene degrading activity than the ones which were immobilized on agar-agar or free cells.     

Plant protection and rhizosphere colonization of barley by seed inoculated herbicide degrading Burkholderia (Pseudomonas) cepacia DBO1(pRO101) in 2,4-D contaminated soil

The 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterium, Burkholderia cepacia (formerly Pseudomonas cepacia) DBO1(pRO101) was coated on non-sterile barley (Hordeum vulgare) seeds, which were planted in two non-sterile soils amended with varying amounts of 2,4-D herbicide. In the presence of 10 or 100 mg 2,4-D per kg soil B. cepacia DBO1(pRO101) readily colonized the root at densities up to 10⁷ CFU per cm root. In soil without 2,4-D the bacterium showed weak root colonization. The seeds coated with B. cepacia DBO1(pRO101) were able to germinate and grow in soils containing 10 or 100 mg kg^–1 2,4-D, while non-coated seeds either did not germinate or quickly withered after germination. The results suggest that colonization of the plant roots by the herbicide-degrading B. cepacia DBO1(pRO101) can protect the plant by degradation of the herbicide in the rhizosphere soil. The study shows that the ability to degrade certain pesticides should be considered, when searching for potential plant growth-promoting rhizobacteria. The role of root colonization by xenobiotic degrading bacteria is further discussed in relation to bioremediation of contaminated soils.     

Heterologous expression of the Bacteroides ruminicola xylanase gene in Bacteroides fragilis and Bacteroides uniformis

A cloned xylanase gene from the ruminal bacterium Bacteroides ruminicola 23 was transferred by conjugation into the colonic species Bacteroides fragilis and Bacteroides uniformis by using the Escherichia coli-Bacteroides shuttle vector pVAL-1. The cloned gene was expressed in both species, and xylanase specific activity in crude extracts was found to be at least 1400-fold greater than that found in the B. ruminicola strain. Analysis of crude extract proteins from the recombinant B. fragilis by SDS-PAGE demonstrated a new 60,000 molecular weight protein. The xylanase activity expressed in both E. coli and B. fragilis was capable of degrading xylan to xylooligosaccharides in vitro. This is the first demonstration that colonic Bacteroides species can express a gene from a ruminal Bacteroides species.     

红树林细菌Rhodococcus ruber 1K降解邻苯二甲酸二丁酯的研究

1引言邻苯二甲酸酯类化合物( PAEs)是世界上生产量大、应用面广的人工合成化合物.1933年Waldo Semon首先将邻苯二甲酸二丁酯用于PVC生产,得到了大幅度改性后的商品化树脂.从此,邻苯二甲酸酯作为增塑剂得到广泛应用.由于作为增塑剂的邻苯二甲酸酯与PVC聚合物及其他材料并非通过共价键结合,在产品的使用过程中及处置后很容易被释放到环境中[2,16].塑料制品的全球性大量应用导致邻苯二甲酸酯在环境中普遍存在[6,7].城市污泥中可以普遍检测到PAEs[6,9,13~15,17,20],由于城市污泥的农用导致在农作物或者农产品中也可以检测到PAEs的存在[3~…     

木质素降解菌shu-0801降解玉米废弃物的研究

目的:研究分离到的木质素降解菌降解玉米废弃物效果.方法:利用苯胺蓝法从土壤中分离到木质素降解菌shu-0801.结果:研究表明shu-0801木质素降解菌能够显著提高纤维素的转化,提高纤维素酶的降解效率,还原糖的生成量明显提高,shu-0801菌与玉米秸秆粉共培养,可降解玉米废弃物干重约20%.结论:分离到木质素菌降解木质素效率较高,属巨大芽孢杆菌属.     

Isolation,Identification and Characteristics of an Endophytic Quinclorac Degrading Bacterium Bacillus megaterium Q3

In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography–tandem mass spectrometry (LC-MS/MS). The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity.     

石油生物催化脱硫菌Agrobacterium tumefaciens UP3的分离筛选

从胜利油田被原油污染的土壤中筛选到一株能有效降解模型化合物二苯并噻吩(DBT)的菌株.根据常规的形态分析、生理生化性状及16S rDNA序列分析,将其鉴定为根癌土壤杆菌(Agrobacterium tumefaciens UP3).该菌不能以十二烷、十六烷、液体石蜡和萘作为唯一碳源和能源生长,具有工业应用的潜力.对该菌株DBT降解能力的初步研究表明,54h内可将500mg/L的DBT降解至150mg/L.对降解产物的分析表明,根癌土壤杆菌降解DBT的途径与Kodama路线及4-S路线不同.     

Detection of collagenase activity in oral bacteria

Collagenolytic activity of 12 species of oral bacteria was assessed using two methods of detection. Except for two species, all bacterial strains tested were capable of degrading at least one general protein substrate. Results of collagenolytic activity in a growth assay indicate that Bacteroides gingivalis is the only bacterium capable of degrading collagen when the substrate is sterilized using ethylene oxide. However, if the substrate is sterilized by autoclaving, in the presence or absence of the growth medium, other bacterial species could be shown to be collagenolytic. Collagenolytic activity was also demonstrated when whole or broken cells were used in a [14C]collagen assay. Results from this assay and from inhibition studies indicate that collagenolytic activity can either be the result of the combined activities of both a specific collagenase and nonspecific proteases (B. gingivalis) or nonspecific proteases only (other strains in this study), although in the latter case, the time taken to hydrolyze collagen can be 10 times longer than with a specific collagenase.     

Identification and characterization of chlorpyrifos-methyl and 3,5,6-trichloro-2-pyridinol degrading Burkholderia sp. strain KR100

A chlorpyrifos-methyl (CM) degrading bacterium (designated strain KR100) was isolated from a Korean rice paddy soil and was further tested for its sensitivity against eight commercial antibiotics. Based on morphological, biochemical, and molecular characteristics, this bacterium showed greatest similarity to members of the order Burkholderiales and was shown to be most closely related to members of the Burkholderia cepacia group. Strain KR100 hydrolyzed CM to 3,5,6-trichloro-2-pyridinol (TCP) and utilized TCP as the sole source of carbon for its growth. The isolate was also able to degrade chlorpyrifos, dimethoate, fenitrothion, malathion, and monocrotophos at 300 μg/ml but diazinon, dicrotophos, parathion, and parathion-methyl at 100 μg/ml. The ability to degrade CM was found to be encoded on a single plasmid of ~50 kb, pKR1. Genes encoding resistance to amphotericin B, polymixin B sulfate, and tetracycline were also located on the plasmid. This bacterium merits further study as a potential biological agent for the remediation of soil, water, or crop contaminated with organophosphorus compounds because of its greater biodegradation activity and its broad specificity against a range of organophosphorus insecticides.     

除草剂氟磺胺草醚降解菌FB8的分离鉴定与土壤修复

【目的】从氟磺胺草醚污染土壤分离高效降解菌株,进行分类学鉴定、降解特性及土壤修复能力初步研究,为氟磺胺草醚污染土壤微生物修复提供新的菌株。【方法】通过形态特征、生理生化特征和16S rRNA序列分析方法进行菌株鉴定;通过农药初始浓度、pH值、温度等环境因素的研究得到菌株的最适生长条件;通过敏感作物和靶标杂草的盆栽生测试验,验证菌株对氟磺胺草醚污染土壤的修复能力。【结果】本试验从黑龙江省长期施用氟磺胺草醚的大豆田地中分离出一株能以氟磺胺草醚为唯一碳源生长的细菌FB8,初步鉴定为假单胞菌属(Pseudomonas),该菌株在96 h内对500 mg/L氟磺胺草醚的降解率高达86.75%,其最适生长条件为500 mg/L农药初始浓度、初始pH6.0-8.0、35-37℃,该菌株处理30 d能够显著恢复敏感作物玉米和高粱的各项生物量指标,对氟磺胺草醚浓度为5 mg/kg的土壤修复效果明显。【结论】从黑龙江省污染土壤中筛选得到的高效降解氟磺胺草醚的门多萨假单胞菌Pseudomonas mendocina FB8,盆栽生测试验表明该菌株具有很好的土壤修复作用,可为氟磺胺草醚的生物修复研究提供适宜的菌种资源。     

地衣芽胞杆菌ATCC9945A中γ-聚谷氨酸降解酶基因的克隆、表达及降解性能鉴定

目的:验证在地衣芽胞杆菌ATCC9945A中存在着γ-聚谷氨酸降解酶基因(ywtD),为下一步解决在γ-聚谷氨酸微生物发酵合成过程中产物γ-PGA降解的技术性难题提供依据。方法:通过在pET-28b(+)大肠杆菌表达系统克隆表达地衣芽孢杆菌ATCC9945A中的ywtD基因,对诱导表达条件进行优化,采用SDS-PAGE和Western Blot方法检测目的蛋白的表达,并体外酶解实验验证其活性。结果:PCR扩增得到了一个1 245bp的基因片段,预期编码414个氨基酸,诱导表达后得到一个分子量大小约为45.6 kDa的表达产物。Western Blot分析结果表明ywtD基因得到了有效表达。体外酶解实验表明该表达产物具有降解γ-PGA的活性。结论:证明在地衣芽胞杆菌ATCC9945A中存在着γ-聚谷氨酸降解酶基因。     

菌株DLL-1降解土壤和韭菜中甲基对硫磷的研究

施甲基对硫磷7．5、15和22．5kg·hm^-2(a．i．)时,韭菜中最终平均农药残留量为0．633、1．270和1．901mg·kg^-1,自然降解率分别为98．94％、96．44％和96．04％．施用高效农药残留降解菌剂能显著地降低农药残留的含量,施用75kg·hm^-2降解菌剂时,韭菜与土壤中平均农药残留量分别为0．269、0．099mg·kg^-1,与不施菌对照相比,能使农药进一步降低78．82％和98．68％．降解率随着菌剂用量增加而升高,当用量超过75kg·hm^-2时降解率不再提高．菌剂施用时间以施药后3d为最好．     

High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.