Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods

In contrast to conventional approaches molecular microbiology leads to a deeper understanding of the biodiversity of soil microorganisms. Nevertheless, there is a lack of knowledge regarding the spatial distribution of microbiota in the complex soil matrix and the interaction between the soil structure and microorganisms. DNA analytical methods such as fluorescence in situ hybridization (FISH) are being utilized to improve the characterization of microbial biocoenosis.Micropedological procedures which preserve the soil structure by embedding it with resin, in combination with FISH, allow the localization and identification of soil microorganism diversity in relation to the specific properties of their microhabitats. In this study, FISH was used prior to resin embedding in undisturbed soil samples of four different soils.The polished sections provided visualization of the bound probes as well as the undisturbed soil matrix via fluorescence microscopy. Furthermore, cell counts of active bacteria, locating of hot spots and their relationship to microsites rich in nutrients and water, such as humus or clay minerals, are now easy to perform. This will lead to a better understanding of how soil structure can affect soil microorganisms and vice versa.Derived from the use of 16S rRNA targeted oligonucleotide probes, EUB338 and NON338, the cell counts of FISH-detected bacteria were in the same order of magnitude in the undisturbed and the suspended soil samples. Counterstaining with DAPI showed varying detection rates caused by differing activities of the soil microorganisms.     

多粘芽孢杆菌芽孢荧光原位杂交检测技术研究及其在有机肥发酵中的应用

采用化学和萌发两种预处理方法,对多粘芽孢杆菌SQR21芽孢进行荧光原位杂交(FISH),结合扫描电镜比较不同预处理芽孢表面结构和形态变化。结果表明,两种预处理均可在2 h内完成SQR21芽孢的荧光原位杂交,且萌发预处理比化学预处理杂交效率高,荧光信号强。扫描电镜结果显示,萌发预处理芽孢无裂解,而化学预处理芽孢有不同程度的裂解。将萌发预处理荧光原位杂交用于检测猪粪有机肥中二次发酵的SQR21芽孢,发现在37℃,含水量50%的条件下,2 h后芽孢开始生长,4 h后营养体细胞出现,12 h后营养体细胞有显著优势。本研究建立的芽孢荧光原位杂交检测技术,比平板计数更能准确反映多粘芽孢杆菌芽孢的数量和生长动态,在生物有机肥中芽孢杆菌的检测方面有良好的应用前景。     

Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

In recent years, methods of molecular microbiology have been used for the investigation of soil microbial diversity. Fluorescence in situ hybridization (FISH) represents a method which allows a specific staining and enumeration of soil microorganisms by using fluorescent-labelled oligonucleotide probes. However, the detection of FISH-stained cells is often affected by strong autofluorescence of the background, especially in samples of the top soils.In this study a more efficient FISH-approach coupled with catalyzed reporter deposition (CARD) was adapted to soils. Due to tyramide signal amplification (TSA) the fluorescence intensity has been considerably increased at the target binding site of a probe.Six different soils were investigated to evaluate the effect of sample preparation and pre-treatments, TSA, and the procedure of detection. The results show that both cell permeabilization and TSA are two important factors which improve in situ hybridization of soil microorganisms. Soils with higher clay contents have shown better results when prepared on polycarbonate filters rather than on glass slides.Using specific fluorescence filter systems and dye combinations the detection of hybridized cells was extensively increased compared with the application of monolabelled oligonucleotide probes in regular FISH-analysis. As a result, CARD-FISH-stained cells were suitable for automated counting using digital image analysis. Nevertheless, the counterstain with DAPI had to be analyzed manually as it was strongly affected by autofluorescence.     

Identification and quantification of flavonol glycosides in almond seedcoats using MALDI-TOF MS

Interest in the molecular composition of almonds is growing, due to their popularity in a wide variety of food formulations. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful new technique that can be used to rapidly identify and quantify possible bioactive compounds in these popular tree nuts. Four flavonol glycosides were identified in almond seedcoats for the first time: isorhamnetin rutinoside, isorhamnetin glucoside, kaempferol rutinoside, and kaempferol glucoside. A MALDI-TOF MS methodology was developed using rutin (quercetin-3-rutinoside) as an internal standard to quantitatively determine each of the four flavonol glycosides. Results of MALDI-TOF MS analysis were verified by high performance liquid chromatography.     

小麦背景中披碱草部分染色体的FISH鉴定

为了建立小麦背景中粗穗披碱草(Elymus trachycaulus)和纤毛披碱草(Elymus ciliaris)染色体的跟踪鉴定方法,本研究利用寡聚核苷酸Oligo-pSc119.2-1和Oligo-pTa-535-1为探针的双色荧光原位杂交(FISH)和以(GAA)8为探针的单色FISH,分别对4个小麦-粗穗披碱...     

UHPLC-PDA-ESI/HRMS/MS(n) analysis of anthocyanins, flavonol glycosides, and hydroxycinnamic acid derivatives in red mustard greens (Brassica juncea Coss variety)

An UHPLC-PDA-ESI/HRMS/MS(n) profiling method was used for a comprehensive study of the phenolic components of red mustard greens ( Brassica juncea Coss variety) and identified 67 anthocyanins, 102 flavonol glycosides, and 40 hydroxycinnamic acid derivatives. The glycosylation patterns of the flavonoids were assigned on the basis of direct comparison of the parent flavonoid glycosides with reference compounds. The putative identifications were obtained from tandem mass data analysis and confirmed by the retention time, elution order, and UV-vis and high-resolution mass spectra. Further identifications were made by comparing the UHPLC-PDA-ESI/HRMS/MS(n) data with those of reference compounds in the polyphenol database and in the literature. Twenty-seven acylated cyanidin 3-sophoroside-5-diglucosides, 24 acylated cyanidin 3-sophoroside-5-glucosides, 3 acylated cyanidin triglucoside-5-glucosides, 37 flavonol glycosides, and 10 hydroxycinnamic acid derivatives were detected for the first time in brassica vegetables. At least 50 of them are reported for the first time in any plant materials.     

Fluorescence analysis of copper(II) and zinc(II) binding behaviour of fulvic acids from pig slurry and amended soils

The evaluation of the mechanisms and extent of interaction of Cu(II) and Zn(II) with fulvic acids (FAs) is of importance for understanding the mobility and bioavailability of these metals in pig slurry (PS)‐amended soils. In this work, a fluorescence titration method and a single site model were used to characterize the interaction of Cu(II) and Zn(II) with FAs isolated from PS, from soils amended with 90 and 150 m³ ha⁻¹ year⁻¹ of PS for 7 years and from the corresponding unamended soil. The binding capacities of FAs and the strengths of metal ion‐FA complexes were larger for Cu(II) than for Zn(II). With respect to the unamended control soil FA, PS‐FA was characterized by smaller binding capacities and stability constants. The binding capacities and affinities of PS‐amended soil FA were intermediate between those of unamended soil FA and PS‐FA, and tended to decrease with increasing amounts of PS applied to soil, thus suggesting a partial incorporation of FA fractions of PS into native soil FA.     

Localization of bacteria in lichens from Alpine soil crusts by fluorescence in situ hybridization

Lichens are prominent components of many biological soil crusts. Owing to their persistence, lichen thalli create microhabitats for other microbes. Here, the structure of bacterial communities at the thallus–soil interface in lichen soil crusts was studied by using fluorescence in situ hybridization (FISH), confocal laser scanning microscopy (CLSM) and 3D image reconstruction. Terricolous lichen thalli above the tree-line in open habitats of the Austrian Alps were sampled. We selected six lichen species associated with green algal photobionts: Arthrorhaphis citrinella, Baeomyces placophyllus, B. rufus, Icmadophila ericetorum, Psora decipiens and Trapeliopsis granulosa. Alphaproteobacteria and Acidobacteria are predominant in these soil crust lichens, where the latter are frequently present in the lower part of lichen thalli and in the hypothallosphere. In the inconspicuous thallus structures of Arthrorhaphis citrinella, Baeomyces rufus, Icmadophila ericetorum and Trapeliopsis granulosa we observed association of bacteria with algal cells in soil particles and on the outer surface of the mycobiont–photobiont aggregates. We found bacterial cells intermixed with photobiont cells in the lower part of the lichen thalli and as small colonies on the surface of the squamules of Baeomyces placophyllus and Psora decipiens. Moreover, technical issues of performing FISH and confocal microscopy with biological soil crusts are discussed.     

Identification of flavonol and xanthone glycosides from mango (Mangifera indica L. Cv. "Tommy Atkins") peels by high-performance liquid chromatography-electrospray ionization mass spectrometry

Flavonol O- and xanthone C-glycosides were extracted from mango (Mangifera indica L. cv. "Tommy Atkins") peels and characterized by high-performance liquid chromatography-electrospray ionization mass spectrometry. Among the fourteen compounds analyzed, seven quercetin O-glycosides, one kaempferol O-glycoside, and four xanthone C-glycosides were found. On the basis of their fragmentation pattern, the latter were identified as mangiferin and isomangiferin and their respective galloyl derivatives. A flavonol hexoside with m/z 477 was tentatively identified as a rhamnetin glycoside, which to the best of our knowledge, has not yet been reported in mango peels. The results obtained in the present study confirm that peels originating from mango fruit processing are a promising source of phenolic compounds that might be recovered and used as natural antioxidants or functional food ingredients.     

我国猪粪中四环素类抗生素残留及好氧堆肥消减研究进展

我国是世界生猪养殖第一大国,四环素类抗生素在生猪养殖中普遍使用,其中大量以原体或代谢物形式排出体外,对生态环境和人体健康产生极大风险.通过梳理国内相关研究结果,综述了猪粪中四环素类抗生素残留水平及其对土壤和作物的污染风险,分析了好氧堆肥技术对猪粪中四环素类抗生素的消减效率及其影响因素,提出了未来需要重点研究的方向.结果...     

Determination of triterpene glycosides in sea cucumber (Stichopus japonicus) and its related products by high-performance liquid chromatography

A creative and sensitive method has been developed for the determination of triterpene glycosides concentrations in sea cucumber ( Stichopus japonicus) and related products by using d-quinovose (6-deoxyglucose) as the measurement standard by reverse-phase high-performance liquid chromatography (HPLC) and variable-wavelength detection. d-quinovose, which is a unique monosaccharide in holostane triterpene glycosides, was liberated by acid hydrolysis and precolumn derivatized by 1-phenyl-3-methyl-5-pyrazolone (PMP). PMP-quinovose was analyzed by HPLC with 22% acetonitrile in 0.05 M KH2PO4 aquatic solution (pH 5.2) as mobile phase. The calibration curves of d-quinovose were linear within the range of 6.56-164 mg/L (r(2) > 0.995). The contents of triterpene glycosides in various S. japonicus products were determined after appropriate pretreatment methods. The concentration of triterpene glycosides was calculated by the formula C = C(qui) x alpha (alpha = 8.5). The result showed that this method was a simple, rapid, and stable method for the determination of triterpene glycosides in S. japonicus products.     

Characterization of phytoecdysteroid glycosides in Meadowfoam (Limnanthes alba) seed meal by positive and negative ion LC-MS/MS

Meadowfoam ( Limnanthes alba) is an oilseed crop grown in western Oregon. The seed meal has potential value as a biopesticide due to glucosinolate degradation products and phytoecdysteroids, a group of polyhydroxylated triterpenoids with potent activities as arthropod molting hormones. Liquid chromatography in combination with tandem mass spectrometry operated in the precursor ion mode revealed the presence of four ecdysteroid glycosides in meadowfoam seed meal. The carbohydrate sequence and the identity of the ecdysteroid aglycones, ponasterone A and 20-hydroxyecdysone, were determined by product ion scanning. Ecdysteroids were detected in the negative ion mode as [M + formate] (-) ions, which yielded [M - H] (-) and alpha-cleavage fragments with retention of hydroxyl groups in MS/MS experiments (not seen in the positive ion mode), allowing the determination of the number of hydroxyl groups in the side chain and in the steroid ring system. MS/MS of glycoside ions ([MH] (+) or [M + formate] (-)) provided carbohydrate sequence information.     

Taxonomic relationships and interspecific hybridization in the genus Lolium (grasses)

Phylogenetic trees of the 8 species of the genus Lolium and of Festuca pratensis have been derived from frequency data at 13 isozyme loci using different distance algorithms. The best tree was obtained by the distance-Wagner method with the Cavalli-Sforza and Edwards chord distance. This tree appears robust when tested by bootstrap resampling of loci. This confirmed previous knowledge on species relationships in the genus Lolium, with supplementary data on the taxonomic position of the less studied L. persicum and L. canariense. Attempts were made to hybridize 4 Lolium species and F. pratensis. True interspecific hybrids, as confirmed by isozyme markers, were obtained for L. perenne x L. temulentum, L. temulentum x L. rigidum, L. temulentum x L. canariense and L. canariense x F. pratensis. This is the first report of this new form of Festulolium, which was obtained at a fairly high frequency, giving argument to a possible genetic proximity between L. canariense, an endemic species restricted to Atlantic islands, and F. pratensis, which has a more widespread, northern distribution. However, chromosome pairing analysis at meiosis did not support this conclusion, as the F1 L. canariense x F. pratensis definitely showed a higher level of asynapsis compared to that reported for L. perenne x F. pratensis. The apparently close relation between L. canariense and F. pratensis seen on the tree is therefore postulated to be an artefact, due to the low number of loci studied.     

Wheat flour enzymatic amylolysis monitored by in situ (1)H NMR spectroscopy

Starch enzymatic degradation caused by endogenous hydrolases is studied by in situ NMR spectroscopy on a set of hard and soft wheat flours. The results obtained by two different techniques (HR-MAS and (1)H NMR in solution) are analyzed in terms of a Michaelis-Menten kinetic phenomenological model taking into account the presence of endogenous enzymes and their eventual inactivation. The parameters resulting from the best fit of all experimental data to the kinetic model equations are submitted to a multivariate statistical analysis to assess the role of the oligosaccharides release in distinguishing between hard and soft wheats.     

应用双分子荧光互补(BiFC)方法分析烟草中介体亚基之间的互作

中介体是一种大分子蛋白复合物,中介体亚基之间的相互作用是中介体复合物在真核生物的转录调控中发挥作用的基础。本研究利用同源搜索,克隆了烟草(Nicotiana tabacum)中介体亚基基因NtMed6、NtMed18和NtMed21,测序结果表明NtMed6、NtMed18和NtMed21与拟南芥(Arabidopsisthaliana)中介体同源基因的序列一致性分别为69.46%、76.91%和77.01%。通过筛选适宜的侵染培养基优化了农杆菌介导的烟草叶片瞬时表达进行亚细胞定位方法,分析了linker序列对亚细胞定位结果的影响。发现以YEB+100mmol/LAS和AA+100mmol/LAS为侵染培养基时荧光强度大,并且表达荧光的细胞多;构建融合表达载体时添加5个氨基酸编码序列的linker提高了融合蛋白亚细胞定位结果的可靠性。烟草中介体亚基亚细胞定位表明,NtMed8、NtMed18、NtMed6和NtMed21定位在细胞核和细胞质内,但主要在细胞核里。为进一步证实NtMed8属于烟草中介体亚基,同时研究NtMed8与其它亚基的相互作用,构建了35S驱动的含有EYFPN-端1-173氨基酸和C-端151-238氨基酸编码序列标签的融合表达载体(pNYE和pCYE)。把NtMed8、NtMed18、NtMed6和NtMed21的全长ORF亚克隆到相应的载体上,共转化烟草(Nicotiana benthamiana)叶片,结果表明,NtMed8与NtMed18存在互作,同时还观察到NtMed8与NtMed6的互作以及NtMed18与NtMed6的互作。BiFC用于检测蛋白之间的互作是一种快捷有效的方法,能够应用于中介体亚基之间结构联系的研究。     

猪粪中3种四环素类抗生素在土壤中的动态变化及降解途径

采用室内模拟培养试验,研究了180 d内不同用量猪粪中3种四环素类抗生素（TCs）（包括四环素TTC,土霉素OTC,金霉素CTC）在土壤中降解的动态变化规律及降解途径。结果表明,猪粪中3种四环素类抗生素进入土壤后含量均呈现前期迅速下降,中后期减缓的规律,但不同种类和用量处理的变化速率和减少幅度有显著差异（P0.05）。180d时,猪粪处理土壤中的降解率为金霉素土霉素四环素,平均半衰期为17.43d、31.32d、49.48d。降解率与猪粪用量呈负相关,同培养时间呈正相关。猪粪中抗生素在土壤中的降解率要高于纯品抗生素,降解率的增加以外源微生物降解为主,外源微生物降解对四环素的作用最好。综上所述,随着培养时间的延长,猪粪中四环素类抗生素在土壤中能随微生物降解等作用而逐渐减少,但短期内仍可能产生环境危害。     

Domestic processing of onion bulbs (Allium cepa) and asparagus spears (Asparagus officinalis): effect on flavonol content and antioxidant status.

Two commonly consumed plant foods, onion bulbs and asparagus spears, were subjected to typical domestic processing, including chopping, maceration, and boiling. The impact of these processes on flavonol content was assessed. Further, the consequences of these processes on the antioxidant capacity of the tissues were evaluated with the beta-carotene bleaching method. Chopping significantly affected rutin content in asparagus, yielding an 18.5% decrease in 60 min; but in onions, quercetin 3,4'-diglucoside (Q(DG)) and quercetin 4'-glucoside (Q(MG)) were virtually unaffected by chopping. Boiling for 60 min had more severe effects, as it caused overall flavonol losses of 20.6 and 43.9% in onions and asparagus, respectively. Chopping of tissues did not considerably influence the antioxidant capacity, but boiling did provoke notable changes.