Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples

Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II.     

Development of a Real-Time PCR assay for quantitative assessment of uncultured freshwater zoosporic fungi

Recently, molecular environmental surveys of the eukaryotic microbial community in lakes have revealed a high diversity of sequences belonging to uncultured zoosporic fungi. Although they are known as saprobes and algal parasites in freshwater systems, zoosporic fungi have been neglected in microbial food web studies. Recently, it has been suggested that zoosporic fungi, via the consumption of their zoospores by zooplankters, could transfer energy from large inedible algae and particulate organic material to higher trophic levels. However, because of their small size and their lack of distinctive morphological features, traditional microscopy does not allow the detection of fungal zoospores in the field. Hence, quantitative data on fungal zoospores in natural environments is missing. We have developed a quantitative PCR (qPCR) assay for the quantification of fungal zoospores in lakes. Specific primers were designed and qPCR conditions were optimized using a range of target and non-target plasmids obtained from previous freshwater environmental 18S rDNA surveys. When optimal DNA extraction protocol and qPCR conditions were applied, the qPCR assay developed in this study demonstrated high specificity and sensitivity, with as low as 100 18S rDNA copies per reaction detected. Although the present work focuses on the design and optimization of a new qPCR assay, its application to natural samples indicated that qPCR offers a promising tool for quantitative assessment of fungal zoospores in natural environments. We conclude that this will contribute to a better understanding of the ecological significance of zoosporic fungi in microbial food webs of pelagic ecosystems.     

CARD-FISH技术及其在微生物生态学研究中的应用

催化报告沉积荧光原位杂交技术(Catalyzed reporter deposition-fluorescence in situ hybridization,CARDFISH)是基于传统的FISH技术发展而来,由于其较高的灵敏度及稳定性,可以检测微生物的rRNA、mRNA和DNA上的目标基因等,获得环境微生物的群落及功能信息,现已成为微生物生态学研究领域中的重要技术手段。近些年,CARD-FISH与同位素示踪技术、纳米二次离子质谱技术(Nano SIMS)、扫描电子显微镜(SEM)、流式细胞仪等技术方法的联合使用,不仅可以研究复杂环境中微生物的物种组成、数量及其高分辨形态学信息,而且可以获得微生物在单细胞水平的生理代谢信息及其活性,对在单细胞水平认识原位环境微生物的生理生态功能具有重要意义。本文重点介绍了CARD-FISH的技术路线和要点,并探讨CARD-FISH与相关技术联用在环境微生物生态学研究中的应用及进展。     

Fluorescence in situ hybridization for intracellular localization of nifH mRNA

Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.     

Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives

The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments.     

CARD-FISH and confocal laser scanner microscopy to assess successional changes of the bacterial community in freshwater biofilms

Bacterial community composition was assessed during riverine biofilm development by the Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in combination with Confocal Laser Scanning Microscopy. Using artificial substrates, it was possible to follow the dynamics of specific bacterial clusters, while maintaining the unaltered structure and architecture of the biofilm.     

Crystal ball: Fluorescence in situ hybridization in the age of super-resolution microscopy

Super-resolution microscopy encompasses a suite of cutting edge microscopy methods able to surpass the resolution limits of light microscopy. The recent commercial availability of super-resolution microscopy is advancing many fields of biology. In this crystal ball forward look, we briefly examine the perspectives of combining super-resolution microscopy and fluorescence in situ hybridization (FISH). We strongly believe, based on first evidence presented here, that using super-resolution microscopy in environmental microbiology has the potential to reshape the way we analyze the results obtained with FISH, by improving both the localization and quantification of target molecules.     

Development of rRNA and rDNA-targeted probes for fluorescence in situ hybridization to detect Heterosigma akashiwo (Raphidophyceae)

Heterosigma akashiwo (Hada) is a fragile, fish-killing alga. Efforts to understand and prevent blooms due to this harmful species to mitigate the impact on aquaculture require the development of methods for rapid and precise identification and quantification, so that adequate warning of a harmful algal bloom may be given. Here, we report the development and application of rRNA and rDNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH) to aid in the detection and enumeration of H. akashiwo. The designed probes were species specific, showing no cross-reactivity with four common HAB causative species: Prorocentrum micans Ehrenberg, P. minimum (Pavillard) Schiller, Alexandrium tarmarense (Lebour) Balech, and Skeletonema costatum (Greville) Cleve, or with four other microalgae, including Gymnodinium sp. Stein, Platy-monas cordiformis (Karter) Korsch, Skeletonema sp.1 Greville and Skeletonema sp.2. The rRNA-targeted probe hybridized to cytoplasmic rRNA, showing strong green fluorescence throughout the whole cell, while cells labeled by rDNA-targeted probe exhibited exclusively fluorescent nucleus. The detection protocols were optimized and could be completed within an hour. For rRNA and rDNA probes, about a corresponding 80% and 70% of targeted cells could be identified and quantified during the whole growth circle, despite the inapparent variability in the average probe reactivity. The established FISH was proved promising for specific, rapid, precise, and quantitative detection of H. akashiwo.     

Novel engineering controls to increase leachate contaminant degradation by refuse: From lab test to in situ engineering application

Here we provide direct evidence through a series laboratory and field-scale experiments using different age refuse to treat landfill leachate that aged refuse exhibits increased leachate contaminants removal ability with refuse stabilization time addition. Ten-years aged refuse showed best contaminant removal in a laboratory-scale test, removing 70.0% (8340.0-2540.0 mg/L) chemical oxygen demand (COD) and 75.0% (910.0-215.0 mg/L) ammonium-N, as well as removing 61.5-67.0% COD and 50.4-58.1% ammonium-N with variable COD (9948.0-12286.0 mg/L) and NH₃-N (780.0-1184.0 mg/L) in a field-scale test, respectively. When the 10-years aged refuse was disinfected by 20% NaClO (wt%), COD, biochemical oxygen demand (BOD₅), total nitrogen (TN), and ammonium-N removal showed a dramatic decrease throughout operation time from 84.4-86.2% to 15.2-34.5%, 94.4-99.8% to 26.2-54.4%, 31.2-33.9% to 2.1-10.1%, and 88.5-90.1% to 1.5-14.5%, respectively, suggesting biodegradation is the dominant contaminant removal. Based on this finding, a 3-stages (8 years) age refuse bioreactor (ARB) was constructed to treat leachate and ARB efficiently reduced chemical oxygen demand (COD) from 5478.0-10842.0 mg/L to 261.0-1020 mg/L (87.8-96.2% removal), ammonium-N from 811.4-1582.0 mg/L to 8.5-43.3 mg/L (96.9-99.4%), respectively, in 18 months running. In summary, the present studies suggest that increased leachate contaminant biodegradation ability of aged refuse could be used directly to create an engineering approach to treat leachate with operational and economic advantages.     

Development of Enterobacter aerogenes fuel cells: From in situ biohydrogen oxidization to direct electroactive biofilm

This study described an Enterobacter aerogenes-catalyzed microbial fuel cell (MFC) with a carbon-based anode that exhibited a maximum power density of 2.51 W/m³ in the absence of artificial electron mediators. The MFC was started up rapidly, within hours, and the current generation in the early stage was demonstrated to result from in situ oxidation of biohydrogen produced by E. aerogenes during glucose fermentation. Over periodic replacement of substrate, both planktonic biomass in the culture liquid and hydrogen productivity decreased, while increased power density and coulombic efficiency and decreased internal resistance were unexpectedly observed. Using scanning electron microscopy and cyclic voltammetry, it was found that the enhanced MFC performance was associated with the development of electroactive biofilm on the anodic surface, proposed to involve an acclimation and selection process of E. aerogenes cells under electrochemical tension. The significant advantage of rapid start-up and the ability to develop an electroactive biofilm identifies E. aerogenes as a suitable biocatalyst for MFC applications.     

Localization of strawberry (Fragaria x ananassa) and Methylobacterium extorquens genes of strawberry flavor biosynthesis in strawberry tissue by in situ hybridization

Strawberry flavor is one of the most popular fruit flavors worldwide, with numerous applications in the food industry. In addition, the biosynthetic origin of the most important strawberry flavor components, such as 2,5-dimethyl-4-hydroxy-2H-furan-3-one (DMHF), is a challenging research area. DMHF's precursor, 2-hydroxy-propanal (or lactaldehyde), is biosynthesized by the endophytic bacterium Methylobacterium extorquens (M. extorquens). In particular, the alcohol dehydrogenase (ADH) enzymes of M. extorquens are involved in the biogenesis of DMHF precursors since they have the capacity to oxidize the strawberry-derived 1,2-propanediol to lactaldehyde. In this study, the expression of the endophytic ADH and the plant DMHF biosynthesis genes was examined in the tissues of raw and ripe strawberry receptacles by in situ hybridization. The presence of endophytic bacteria was studied in the same tissues by probes targeting bacterial 16S ribosomal ribonucleic acid. Hybridization signals of probes specific for endophytic ADH and plant DMHF biosynthesis genes, as well as bacteria-specific probes, were detected in the same locations. The probes were localized near the plasma membranes or intercellular spaces of cortical and vascular tissues of the receptacle, and intracellularly in the tissues of achenes. By localizing the expression of the endophytic methanol ADH and plant DMHF biosynthesis genes to the same tissues, we have reinforced our original hypothesis that an intimate symbiotic relationship between strawberry and endophytic cells exists and leads to the biosynthesis of DMHF.     

黑胸散白蚁肠道共生锐滴虫目鞭毛虫的多样性分析与原位杂交鉴定

低等木食性白蚁肠道内的鞭毛虫在纤维素降解过程中扮演着重要的角色。黑胸散白蚁Reticulitermes chinensis Snyder是一种广泛分布于我国的低等木食性白蚁,然而目前对于其肠道内的共生鞭毛虫却鲜见报道。采用锐滴虫目18S rDNA特异引物扩增鞭毛虫18S rRNA 基因并构建文库,对得到的基因进行系统发育多样性分析。针对得到的序列设计特异性的荧光探针,用荧光原位杂交技术对锐滴虫目鞭毛虫进行了鉴定。从黑胸散白蚁肠道得到11个锐滴虫目鞭毛虫18S rDNA序列,它们之间的相似性为86.9%-99.3%。系统发育分析表明,锐滴虫目鞭毛虫主要属于Dinenympha和Pyrsonympha两个属。应用荧光原位杂交技术鉴定出了Dinenympha parva、Dinenympha exilis和Pyrsonympha sp.三种锐滴虫。研究表明,在黑胸散白蚁肠道共生的锐滴虫为Dinenympha和Pyrsonympha属的鞭毛虫。     

The effect of juvenile hormone on prothoracic gland function during the larval-pupal development of Manduca sexta: An in situ and in vitro analysis

The application of juvenile hormone I or ZR 512 to neck-ligated, day-5 fifth instar (V₅) larvae reduced the time to pupation in a dose-dependent manner when compared to neck-ligated controls treated with methyl epoxy stearate. Haemolymph ecdysteroid titres determined by radioimmunoassay (RIA) reflected the ability of juvenile hormone I and ZR 512 to stimulate larval-pupal development, i.e. the ecdysteroid titres were similar to those of normally developing larvae although the ecdysteroid peak elicited by ZR 512 lagged that in the normal titre by 1 day, while that elicited by juvenile hormone I lagged the ecdysteroid peak in normal larvae by 2 days. Neck-ligated V₅ larvae that were untreated ultimately pupated and the haemolymph ecdysteroid peak eliciting pupation in these animals was 7 μg/ml haemolymph, almost double that of normal animals and ZR 512- and juvenile hormone I-treated, ligated larvae. The data indicated that juvenile hormone I does stimulate the prothoracic glands but to determine whether this stimulation was direct or indirect, an in vitro approach was taken. Prothoracic glands from V₅, V₆ and V₇ larvae were incubated in vitro under conditions in which they could be stimulated by prothoracicotropic hormone, and were exposed to concentration of free juvenile hormones I, II, III or ZR 512 ranging from 10^?5M to 10^?10M. In no case were the prothoracic glands stimulated in a dose-dependent manner that would be indicative of hormone activation. Similar results were obtained when juvenile hormone bound to binding protein was incubated with the prothoracic glands. Studies with the acids of the three juvenile hormone homologues revealed them to be ineffective in activating prothoracic glands, although juvenile hormone III acid does appear to inhibit the synthesis of ecdysone by day-0 pupal prothoracic glands. The significance of the latter effect is unknown. It is concluded from these data that juvenile hormone can, indeed, activate late larval prothoracic glands in situ, but does so indirectly.     

Electrophoretic study of heating in situ on proteins and enzymes in germinated Arachis hypogaea cotyledons: Comparison with dormant seed

-Cotyledons from 5-day germinated seed of Arachis hypogaea were heated in a moisturized chamber at temperatures from 25 to 121°. Proteins were extracted in phosphate buffer and analyzed with horizontal starch gel electrophoresis to determine the effect of heat on migration patterns of soluble proteins, malate dehydrogenase, glutamate dehydrogenase, leucine aminopeptidase, peroxidases and nonspecific esterases. The intensity of staining of soluble proteins from 5-day cotyledons began decreasing at 80–90°; very little staining occurred at 100° with the exception of a distinct band at R_f 1·0. Glutamate dehydrogenase and benzidine peroxidase retained some activity at 80° but other enzymes were inactivated at temperatures near 65°. Differential heat sensitivities of isoenzymes were obvious. Heat did not alter the R_f values of the bands of soluble proteins or enzymes but influenced the intensity of staining. Two-year storage at 4° of viable seed and 33-month storage at -10° of frozen extracts from dormant seed had no influence upon migration patterns of soluble proteins and enzymes assayed.     

Phylogenetic characterization and in situ detection of bacterial communities associated with seahorses (Hippocampus guttulatus) in captivity

Although there are several studies describing bacteria associated with marine fish, the bacterial composition associated with seahorses has not been extensively investigated since these studies have been restricted to the identification of bacterial pathogens. In this study, the phylogenetic affiliation of seahorse-associated bacteria was assessed by 16S rRNA gene sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rRNA analysis. Both methods revealed that Vibrionaceae was the dominant population in Artemia sp. (live prey) and intestinal content of the seahorses, while Rhodobacteraceae was dominant in water samples from the aquaculture system and cutaneous mucus of the seahorses. To our knowledge, this is the first time that bacterial communities associated with healthy seahorses in captivity have been described.     

Detecting condylar contact loss using single-plane fluoroscopy: A comparison with in vivo force data and in vitro bi-plane data

Knee contact mechanics play an important role in knee implant failure and wear mechanics. Femoral condylar contact loss in total knee arthroplasty has been reported in some studies and it is considered to potentially induce excessive wear of the polyethylene insert.Measuring in vivo forces applied to the tibial plateau with an instrumented prosthesis is a possible approach to assess contact loss in vivo, but this approach is not very practical. Alternatively, single-plane fluoroscopy and pose estimation can be used to derive the relative pose of the femoral component with respect to the tibial plateau and estimate the distance from the medial and lateral parts of the femoral component towards the insert. Two measures are reported in the literature: lift-off is commonly defined as the difference in distance between the medial and lateral condyles of the femoral component with respect to the tibial plateau; separation is determined by the closest distance of each condyle towards the polyethylene insert instead of the tibia plateau.In this validation study, lift-off and separation as measured with single-plane fluoroscopy are compared to in vivo contact forces measured with an instrumented knee implant. In a phantom study, lift-off and separation were compared to measurements with a high quality bi-plane measurement.The results of the in vivo contact-force experiment demonstrate a large discrepancy between single-plane fluoroscopy and the in vivo force data: single-plane fluoroscopy measured up to 5.1 mm of lift-off or separation, whereas the force data never showed actual loss of contact. The phantom study demonstrated that the single-plane setup could introduce an overestimation of 0.22 mm±±0.36 mm. Correcting the out-of-plane position resulted in an underestimation of medial separation by −0.20 mm±±0.29 mm.In conclusion, there is a discrepancy between the in vivo force data and single-plane fluoroscopic measurements. Therefore contact loss may not always be determined reliably by single plane fluoroscopy analysis.     

Isolation of oligodendroglial cells from young and adult whole rat brains using an in situ generated percoll density gradient

A method for the isolation of oligodendroglial cells from young and adult whole rat brains, using a Percoll density gradient is presented. The minced tissue, incubated in a balanced salt solution containing 0.1% trypsin is further dissociated by forcing it through nylon screens to 145 and 74 μm pore size. The crude suspension is then mixed with an isosmotic Percoll solution and centrifuged for 15 min. An in situ generated density gradient allows the separation of five bands, only one of which (Band C) lying between δ1.050 and δ1.062 contains cellular elements. The isolated cells show the typical morphological characteristics of oligodendroglia.A detailed morphological study of the cells isolated from whole brains of 10-, 30- and 120-day old rats is presented for the first time in the literature and immunocytochemical characterization is carried out using specific (antigalactocerebroside) and non specific (anti-glial fibrillary acidic protein) anti-sera.The method is simple and rapid and isosmotic conditions are maintained throughout, resulting in a better preservation of cell integrity. It represents an improvement over the two previous methods described in the literature and will be useful for studying different developmental events (biochemical and morphological) occurring in oligodendroglial cells at early stages of myelin formation.