Ecophysiological and Phylogenetic Studies of Nevskia ramosa in Pure Culture

During the last 100 years, the neuston bacterium Nevskia ramosa has been described several times. This bacterium forms conspicuous rosette-like microcolonies at the air-water interface. In this study, pure cultures of Nevskia ramosa were obtained for the first time, from a bog lake (strain Soe1, DSMZ 11499^T) and a freshwater ditch (strain OL1, DSMZ 11500). The isolates showed special adaptations to life in the epineuston. They formed hydrophobic surface films with a dull appearance. N. ramosa is sensitive to UV radiation but revealed a very effective photorepair mechanism. Exposure to light at a wavelength of 350 nm after UV treatment raised the number of surviving cells by several orders of magnitude. The isolates grew with a broad range of organic substrates. Surface films were formed only in the absence of combined nitrogen; however, nitrogenase activity was not detected. It appears that during growth at the air-water interface the cells benefit from trapping ammonia from the air. The G+C content of the DNA was 67.8 and 69.0 mol% for strains Soe1 and OL1, respectively. The slight difference was confirmed by enterobacterial repetitive intergenic consensus PCR. The 16S rRNA sequences revealed 99.2% similarity. Thus, both isolates belong to the same species. The phylogenetic analysis indicated that Nevskia is a member of the gamma-subclass Proteobacteria that has no known close relatives.Some morphologically conspicuous bacteria were observed in the 19th century but still have not been isolated in pure culture. In 1892, Famintzin (7) described Nevskia ramosa from the water surface of an aquarium in the botanical garden of St. Petersburg, Russia. The typical microcolonies consist of flat rosettes with a bush-like appearance on the water surface. The rosettes are colonies of dichotomously branched slime stalks with rod-shaped, slightly bent cells in the tips. The cells contain refractile globules, which were presumed to be ethereal oil (7), sulfur globules (12), or fat droplets (3). The slime stalks consist of polysaccharides (3) and sometimes appear to contain iron and aluminum encrustations (11).Enrichments of Nevskia-like cells in lake water supplied with lactate were described by Babenzien (1–4). He observed the following life cycle of N. ramosa. Young motile cells develop submersed, then adsorb to the water surface, lose the polar flagellum, and form a hyaline slime stalk on the concave side of the cell. When a cell multiplies by binary fission, branching of the stalk occurs. The resulting flat rosette can reach a size of 70 μm in diameter.Since pure cultures have not been available, little is known about the physiology, phylogeny, and ecology of Nevskia. It was assumed that Nevskia is oligocarbophilic (14). Tests with the nitrification inhibitor nitrapyrin gave no indications that the cells oxidize ammonia (16). N. ramosa was assumed to be related to the stalk-forming genera Caulobacter and Gallionella or to the sulfur-oxidizing Thiobacterium. In Bergey’s manual (4) N. ramosa was affiliated with the budding and/or appendaged bacteria.In addition to its conspicuous morphology, the typical habitat of N. ramosa prompted us to initiate the present investigation. The water-air interface is a very special environment, characterized by high surface tension and a relatively high hydrophobicity. Organic compounds and various typical bacteria are enriched in this zone. The living community is called the neuston (18, 21). Depending on whether they adsorb to the underside or the top of the water surface, organisms belong to the hyponeuston or epineuston, respectively. This habitat requires special adaptations with respect to adsorption, substrate uptake, and UV tolerance.In our study we have isolated N. ramosa in pure culture and carried out ecophysiological and phylogenetic characterizations. We found several adaptions to life in the epineuston in this interesting bacterium.     

Nitrapyrin-ammonium combination induces rapid multiplication of mixed cultures of the stalked bacterium Nevskia ramosa famintzin and other heterotrophic bacteria

Nevskia ramosa, a bacterium that is very difficult to grow in artificial culture media in its recognizable and natural habit was induced to grow and multiply rapidly in mixed culture in an amended ASM medium. ASM liquid medium, an inorganic mineral medium, amended with 0.5 g ml^-1 of nitrapyrin and various levels of ammonium chloride (25–100 M) produced very significant enrichment of Nevskia ramosa within 24 h, permitting formation of its characteristic bushy dichotomously branched, stalked colonies with the bacterial cells at the apices of branches. ASM medium amended with either nitrapyrin or ammonium singly failed to produce growth of N. ramosa. The nitrapyrinammonium combination in ASM medium also produced a significant increase in growth of other heterotrophic bacteria. Our results should be of value to bacteriologists interested in studying N. ramosa, a species which has received little attention thus far.     

In vivo development of spores of Absidia ramosa.

Approximately 10(6) spores of Absidia ramosa were inoculated intravenously into normal and cortisone pretreated mice. At subsequent time intervals the liver, lungs and kidneys were removed and examined for fungal localization and growth. In normal mice, spore germination and continued hyphal growth was restricted to the kidneys-evidence of germination not being visible until around 30h post inoculation. Cortisone therapy allowed germination of spores in the lung and kidney by 7h but subsequent hyphal growth in the lung was severely restricted compared with the kidney where extensive hyphal growth occurred. Germination of spores in the liver of cortisone treated animals was slow, not becoming apparent until about 40h after inoculation. These results suggest that host defence mechanisms in the form of phagocytosis as well as biochemical inhibitors and/or lack of suitable stimulators are important in preventing germination of introduced fungal spores. Once germination has occurred, it appears that additional as yet undetermined factors play a role in allowing continued growth of the fungus.     

Combined Fluorescent-Chromogenic In Situ Hybridization for Identification and Laser Microdissection of Interphase Chromosomes

Chromosome territories constitute the most conspicuous feature of nuclear architecture, and they exhibit non-random distribution patterns in the interphase nucleus. We observed that in cell nuclei from humans with Down Syndrome two chromosomes 21 frequently localize proximal to one another and distant from the third chromosome. To systematically investigate whether the proximally positioned chromosomes were always the same in all cells, we developed an approach consisting of sequential FISH and CISH combined with laser-microdissection of chromosomes from the interphase nucleus and followed by subsequent chromosome identification by microsatellite allele genotyping. This approach identified proximally positioned chromosomes from cultured cells, and the analysis showed that the identity of the chromosomes proximally positioned varies. However, the data suggest that there may be a tendency of the same chromosomes to be positioned close to each other in the interphase nucleus of trisomic cells. The protocol described here represents a powerful new method for genome analysis.     

Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia

Four isolates, with an optimum temperature of about 30°C and an optimum pH for growth of 6.0-6.5, were recovered from a borehole head of a mineral water aquifer in Portugal and from the stored bottles produced on site. Strains F2-63(T) and F2-178 were yellow-pigmented and formed non-motile rod-shaped cells. Strains G6M-30(T) and G6-54 were whitish-pigmented, translucent and form rod-shaped cells with a polar flagellum. The four strains were strictly aerobic, oxidase and catalase positive. The major fatty acids of strains F2-63(T) and F2-178 were C(18:1)ω7c and C(16:0), and the major fatty acids of strains G6M-30(T) and G6-54 were C(18:1)ω7c and C(16:1)ω7c. Ubiquinone 8 was the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics two new species of the genus Nevskia are described; Nevskia aquatilis represented by strains F2-63(T) (=LMG 26345 =CECT 7897) and F2-178 (=LMG 26344 =CECT 7898) and Nevskia persephonica represented by strains G6M-30(T) (=DSM 24987 =CECT 7975) and G6-54 (=DSM 25048 =CECT 7976).     

Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria

Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. Penetration of the HRP molecule into bacterial cells requires permeabilization procedures that cause high and most probably species-selective cell loss. Here we present an improved protocol for CARD-FISH of marine planktonic and benthic microbial assemblages. After concentration of samples onto membrane filters and subsequent embedding of filters in low-gelling-point agarose, no decrease in bacterial cell numbers was observed during 90 min of lysozyme incubation (10 mg ml⁻¹ at 37°C). The detection rates of coastal North Sea bacterioplankton by CARD-FISH with a general bacterial probe (EUB338-HRP) were significantly higher (mean, 94% of total cell counts; range, 85 to 100%) than that with a monolabeled probe (EUB338-mono; mean, 48%; range, 19 to 66%). Virtually no unspecific staining was observed after CARD-FISH with an antisense EUB338-HRP. Members of the marine SAR86 clade were undetectable by FISH with a monolabeled probe; however, a substantial population was visualized by CARD-FISH (mean, 7%; range, 3 to 13%). Detection rates of EUB338-HRP in Wadden Sea sediments (mean, 81%; range, 53 to 100%) were almost twice as high as the detection rates of EUB338-mono (mean, 44%; range, 25 to 71%). The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment.     

Identification, Characterization, and In Situ Detection of a Fruit-Body-Specific Hydrophobin of Pleurotus ostreatus

Hydrophobins are small (length, about 100 ± 25 amino acids), cysteine-rich, hydrophobic proteins that are present in large amounts in fungal cell walls, where they form part of the outermost layer (rodlet layer); sometimes, they can also be secreted into the medium. Different hydrophobins are associated with different developmental stages of a fungus, and their biological functions include protection of the hyphae against desiccation and attack by either bacterial or fungal parasites, hyphal adherence, and the lowering of surface tension of the culture medium to permit aerial growth of the hyphae. We identified and isolated a hydrophobin (fruit body hydrophobin 1 [Fbh1]) present in fruit bodies but absent in both monokaryotic and dikaryotic mycelia of the edible mushroom Pleurotus ostreatus. In order to study the temporal and spatial expression of the fbh1 gene, we determined the N-terminal amino acid sequence of Fbh1. We also synthesized and cloned the double-stranded cDNA corresponding to the full-length mRNA of Fbh1 to use it as a probe in both Northern blot and in situ hybridization experiments. Fbh1 mRNA is detectable in specific parts of the fruit body, and it is absent in other developmental stages.     

Identification of Nitrite-Reducing Bacteria Using Sequential mRNA Fluorescence In Situ Hybridization and Fluorescence-Assisted Cell Sorting

Sequential mRNA fluorescence in situ hybridization (mRNA FISH) and fluorescence-assisted cell sorting (SmRFF) was used for the identification of nitrite-reducing bacteria in mixed microbial communities. An oligonucleotide probe labeled with horseradish peroxidase (HRP) was used to target mRNA of nirS, the gene that encodes nitrite reductase, the enzyme responsible for the dissimilatory reduction of nitrite to nitric oxide. Clones for nirS expression were constructed and used to provide proof of concept for the SmRFF method. In addition, cells from pure cultures of Pseudomonas stutzeri and denitrifying activated sludge were hybridized with the HRP probe, and tyramide signal amplification was performed, conferring a strongly fluorescent signal to cells containing nirS mRNA. Flow cytometry-assisted cell sorting was used to detect and physically separate two subgroups from a mixed microbial community: non-fluorescent cells and an enrichment of fluorescent, nitrite-reducing cells. Denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of 16S ribosomal RNA (rRNA) genes were used to compare the fragments amplified from the two sorted subgroups. Sequences from bands isolated from DGGE profiles suggested that the dominant, active nitrite reducers were closely related to Acidovorax BSB421. Furthermore, following mRNA FISH detection of nitrite-reducing bacteria, 16S rRNA FISH was used to detect ammonia-oxidizing and nitrite-oxidizing bacteria on the same activated sludge sample. We believe that the molecular approach described can be useful as a tool to help address the longstanding challenge of linking function to identity in natural and engineered habitats.     

Phylogenetic Position and In Situ Identification of Ectosymbiotic Spirochetes on Protists in the Termite Gut

Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp., Stephanonympha sp., and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut protists.     

原位PCR技术及其应用

本文介绍了原位PCR的主要进展、基本步骤,并对其在外源基因检测、基因变异、基因表达及定位等方面的应用作一综述 。     

Hybrid Identification in Clivia(Amaryllidaceae) using Chromosome Banding and Genomic In Situ Hybridization

Giemsa C-banding and genomic in situ hybridization (GISH) wereused to identify parental genomes in hybrids of Clivia(Amaryllidaceae).Of the three groups reputed to be hybrids, onlyC. cyrtanthiflorawas shown to be of hybrid origin. The ‘German hybrids’and ‘Belgian hybrids’ were both shown to be karyotypicallyand genomically similar to C. miniata, and are either selectionsor intraspecific hybrids of that species. Successful genomedifferentiation in F₁hybrids by GISH required high stringencyand high ratios of blocking DNA to probe. The spatial dispositionof different genomes with C-band or GISH markers in the hybridswas investigated in two dimensions on the spread. In five artificiallyproduced hybrids, either C-banding or GISH was used to locatethe position of parental genomes in mitotic metaphase cells.In all cases there was a significant tendency for centromeresof the different parental genomes to occupy two distinct concentricdomains on the metaphase plate. The presence or absence of centromericheterochromatin was not correlated with genome disposition.Results show that chromosome analyses can be a useful way ofidentifying Clivia hybrids in their vegetative phase. Copyright2001 Annals of Botany Company Clivia, genomic in situ hybridization, cultivar origin, parental genome separation     

In Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes

We investigated the in situ spatial organization of ammonia-oxidizing and nitrite-oxidizing bacteria in domestic wastewater biofilms and autotrophic nitrifying biofilms by using microsensors and fluorescent in situ hybridization (FISH) performed with 16S rRNA-targeted oligonucleotide probes. The combination of these techniques made it possible to relate in situ microbial activity directly to the occurrence of nitrifying bacterial populations. In situ hybridization revealed that bacteria belonging to the genus Nitrosomonas were the numerically dominant ammonia-oxidizing bacteria in both types of biofilms. Bacteria belonging to the genus Nitrobacter were not detected; instead, Nitrospira-like bacteria were the main nitrite-oxidizing bacteria in both types of biofilms. Nitrospira-like cells formed irregularly shaped aggregates consisting of small microcolonies, which clustered around the clusters of ammonia oxidizers. Whereas most of the ammonia-oxidizing bacteria were present throughout the biofilms, the nitrite-oxidizing bacteria were restricted to the active nitrite-oxidizing zones, which were in the inner parts of the biofilms. Microelectrode measurements showed that the active ammonia-oxidizing zone was located in the outer part of a biofilm, whereas the active nitrite-oxidizing zone was located just below the ammonia-oxidizing zone and overlapped the location of nitrite-oxidizing bacteria, as determined by FISH.     

Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog

The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 10⁷ and 1.1 × 10⁷ cells g⁻¹ peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.     

Automated Reconstruction Algorithm for Identification of 3D Architectures of Cribriform Ductal Carcinoma In Situ

Ductal carcinoma in situ (DCIS) is a pre-invasive carcinoma of the breast that exhibits several distinct morphologies but the link between morphology and patient outcome is not clear. We hypothesize that different mechanisms of growth may still result in similar 2D morphologies, which may look different in 3D. To elucidate the connection between growth and 3D morphology, we reconstruct the 3D architecture of cribriform DCIS from resected patient material. We produce a fully automated algorithm that aligns, segments, and reconstructs 3D architectures from microscopy images of 2D serial sections from human specimens. The alignment algorithm is based on normalized cross correlation, the segmentation algorithm uses histogram equilization, Otsu's thresholding, and morphology techniques to segment the duct and cribra. The reconstruction method combines these images in 3D. We show that two distinct 3D architectures are indeed found in samples whose 2D histological sections are similarly identified as cribriform DCIS. These differences in architecture support the hypothesis that luminal spaces may form due to different mechanisms, either isolated cell death or merging fronds, leading to the different architectures. We find that out of 15 samples, 6 were found to have 'bubble-like' cribra, 6 were found to have 'tube-like' criba and 3 were 'unknown.' We propose that the 3D architectures found, 'bubbles' and 'tubes', account for some of the heterogeneity of the disease and may be prognostic indicators of different patient outcomes.     

Bioremediation via In Situ Electrotransformation

Bioremediation of polluted sites relies on bacteria to degrade or transform contaminants into less noxious chemicals. To do so, bacteria require genes that encode the degradation enzymes and the capacity to properly express them, which may be lacking in indigenous bacteria. To increase the ability of indigenous bacteria to bioremediate a contaminated site, this research proposes the use of electrotransformation to facilitate bacterial uptake of exogenous degradation genes. As a proof of concept, a lindane degradation gene (linA) located on a broad host-spectrum expression plasmid (pBLN) was introduced into soil bacteria by electroporation both in vitro, in liquid media, and in situ, in soil. In both cases, the electrotransformed bacteria displayed an increase in lindane degradation and an increase in the linA gene copy number. The use of in situ electrotransformation could improve pollutant degradation rates and could provide another tool for bioremediation.     

ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data

Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI–IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI–IMS. This is achieved by combining information from IMS and shotgun proteomics (LC–MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC–MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.