scholarly journals Phylogenetic Affinity of a Wide, Vacuolate, Nitrate-AccumulatingBeggiatoa sp. from Monterey Canyon, California, withThioploca spp

1999 ◽  
Vol 65 (1) ◽  
pp. 270-277 ◽  
Author(s):  
Azeem Ahmad ◽  
James P. Barry ◽  
Douglas C. Nelson
Keyword(s):  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
Sequence Data ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Cold Seeps ◽  
16S Rrna Sequence ◽  
Species Cluster ◽  
Physiological Adaptations

ABSTRACT Environmentally dominant members of the genus Beggiatoaand Thioploca spp. are united by unique morphological and physiological adaptations (S. C. McHatton, J. P. Barry, H. W. Jannasch, and D. C. Nelson, Appl. Environ. Microbiol. 62:954–958, 1996). These adaptations include the presence of very wide filaments (width, 12 to 160 μm), the presence of a central vacuole comprising roughly 80% of the cellular biovolume, and the capacity to internally concentrate nitrate at levels ranging from 150 to 500 mM. Until recently, the genera Beggiatoa andThioploca were recognized and differentiated on the basis of morphology alone; they were distinguished by the fact that numerousThioploca filaments are contained within a common polysaccharide sheath, while Beggiatoa filaments occur singly. Vacuolate Beggiatoa or Thioploca spp. can dominate a variety of marine sediments, seeps, and vents, and it has been proposed (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature [London] 374:713–715, 1995) that members of the genusThioploca are responsible for a significant portion of total marine denitrification. In order to investigate the phylogeny of an environmentally dominant Beggiatoa sp., we analyzed complete 16S rRNA gene sequence data obtained from a natural population found in Monterey Canyon cold seeps. Restriction fragment length polymorphism analysis of a clone library revealed a dominant clone, which gave rise to a putative Monterey Beggiatoa 16S rRNA sequence. Fluorescent in situ hybridization with a sequence-specific probe confirmed that this sequence originated from wideBeggiatoa filaments (width, 65 to 85 μm). A phylogenetic tree based on evolutionary distances indicated that the MontereyBeggiatoa sp. falls in the gamma subdivision of the classProteobacteria and is most closely related to the genusThioploca. This vacuolate Beggiatoa—Thioplocacluster and a more distantly related freshwater Beggiatoaspecies cluster form a distinct phylogenetic group.

scholarly journals A rare case of equine Haemotropic Mycoplasma infection in Nigeria

2021 ◽  
Vol 41 (3) ◽  
pp. 274-286
Author(s):  
A.N Happi ◽  
P.E Oluniyi
Keyword(s):  
16S Rrna ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Findings ◽  
Epidemiological Surveillance ◽  
Response To Treatment ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
16S Rrna Sequence

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted a thorough molecular investigation of suspected haemoparasitic infection given the fluctuating parasitaemia and the low sensitivity and specificity of Light Microscopy (LM) detection of haemoparasitic infections. Blood collected from an adult horse, domiciled at the University of Ibadan Veterinary Teaching Hospital, Ibadan, Nigeria was screened by LM and PCR techniques for haemo-parasites. The 16S rRNA gene of pan-Hemoplasma spp was targeted amplified and sequenced using Sanger automatic sequencing techniques. This case shows the very first molecular evidence of EHM in Africa and Nigeria, and the third case in the World. Microscopic examination of the horse’s blood smear presented with signs of lethargy, inactivity, anorexia and moderate emaciation, showed numerous coccoid-shaped epierythrocytic parasites. Subsequent 16S rRNA sequence data and phylogenetic analyses confirmed the presence of a haemotropic mycoplasma (‘Candidatus M. haemocervae’–like) in the horse. The hemoplasma sequence obtained falls in the same clade with some Candidatus Mycoplasma haemocervae sequences with which it shared more than 98.7% homology. This finding suggests that horses in this geographical region may also be suffering from EHM and calls for the need of epidemiological surveillance of equine hemoplasmosis with emphasis on their clinical, economic, performance and zoonotic implications in the sub-region. Keywords: Nigeria, Horse, Haemotropic mycoplasma, ‘Candidatus M. haemocervae’–like

Ultrastructural and molecular characterization of endosymbionts of the reed beetle genusMacroplea(Chrysomelidae, Donaciinae), and proposal of “CandidatusMacropleicola appendiculatae” and “CandidatusMacropleicola muticae”

2009 ◽  
Vol 55 (11) ◽  
pp. 1250-1260 ◽  
Author(s):  
Gregor Kölsch ◽  
Corinna Matz-Grund ◽  
Bo V. Pedersen
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
Malpighian Tubules ◽  
Rrna Gene ◽  
Beetle Species ◽  
Bacterial Symbionts ◽  
The 16S Rrna Gene

Intracellular bacterial symbionts are known from various insect groups, particularly from those feeding on unbalanced diets, where the bacteria provide essential nutrients to the host. In the case of reed beetles (Coleoptera: Chrysomelidae, Donaciinae), however, the endosymbionts appear to be associated with specialized “glands” that secrete a material used for the beetles’ unusual water-tight cocoon. These glands were discovered over a century ago, but the bacteria they contain have yet to be characterized and placed in a phylogenetic context. Here, we describe the ultrastructure of two endosymbiotic species (“ Candidatus Macropleicola appendiculatae” and “ Candidatus Macropleicola muticae”) that reside in cells of the Malpighian tubules of the reed beetle species Macroplea appendiculata and Macroplea mutica , respectively. Fluorescent in situ hybridization using oligonucleotides targeting the 16S rRNA gene specific to Macroplea symbionts verified the localization of the symbionts in these organs. Phylogenetic analysis of 16S rRNA placed “Candidatus Macropleicola” in a clade of typically endosymbiotic Enterobacteriaceae (γ-proteobacteria). Finally, we discuss the evidence available for the hypothesis that the beetle larvae use a secretion produced by the bacteria for the formation of an underwater cocoon.

scholarly journals Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities

2008 ◽  
Vol 74 (9) ◽  
pp. 2814-2821 ◽  
Author(s):  
Katja Metfies ◽  
Linda K. Medlin
Keyword(s):  
In Situ Hybridization ◽  
Secondary Structure ◽  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rrna Molecule ◽  
The 16S Rrna Gene

ABSTRACT DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.

scholarly journals Natural Communities of Novel Archaea and Bacteria Growing in Cold Sulfurous Springs with a String-of-Pearls-Like Morphology

2001 ◽  
Vol 67 (5) ◽  
pp. 2336-2344 ◽  
Author(s):  
Christian Rudolph ◽  
Gerhard Wanner ◽  
Robert Huber
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fluorescent In Situ Hybridization ◽  
Close Association ◽  
Outer Part ◽  
Rrna Gene ◽  
Rrna Tree ◽  
Gene Sequence Analysis ◽  
String Of Pearls

ABSTRACT We report the identification of novel archaea living in close association with bacteria in the cold (approximately 10°C) sulfurous marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. These microorganisms form a characteristic, macroscopically visible structure, morphologically comparable to a string of pearls. Tiny, whitish globules (the pearls; diameter, about 0.5 to 3.0 mm) are connected to each other by thin, white-colored threads. Fluorescent in situ hybridization (FISH) studies have revealed that the outer part of the pearls is mainly composed of bacteria, with a filamentous bacterium predominating. Internally, archaeal cocci are the predominant microorganisms, with up to 107 cells estimated to be present in a single pearl. The archaea appear to be embedded in a polymer of unknown chemical composition. According to FISH and 16S rRNA gene sequence analysis, the archaea are affiliated with the euryarchaeal kingdom. The new euryarchaeal sequence represents a deep phylogenetic branch within the 16S rRNA tree and does not show extensive similarity to any cultivated archaea or to 16S rRNA gene sequences from environmental samples.

scholarly journals Characterization of Ferroplasma Isolates and Ferroplasma acidarmanus sp. nov., Extreme Acidophiles from Acid Mine Drainage and Industrial Bioleaching Environments

2004 ◽  
Vol 70 (4) ◽  
pp. 2079-2088 ◽  
Author(s):  
Mark Dopson ◽  
Craig Baker-Austin ◽  
Andrew Hind ◽  
John P. Bowman ◽  
Philip L. Bond
Keyword(s):  
16S Rrna ◽  
Yeast Extract ◽  
Mine Drainage ◽  
Sequence Data ◽  
Polyacrylamide Gel Electrophoresis ◽  
Single Species ◽  
The Other ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Ferroplasma Acidarmanus

ABSTRACT Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum YT by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate “Ferroplasma acidarmanus” Fer1T required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42°C and the pH optima were 1.0 to 1.7, and “F. acidarmanus” Fer1T was capable of growing at pH 0. The optimum yeast extract concentration for “F. acidarmanus” Fer1T was higher than that for the other three isolates. Phenotypic results suggested that isolate “F. acidarmanus” Fer1T is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and YT group as a single species. “F. acidarmanus” Fer1T groups separately, and we propose the new species “F. acidarmanus” Fer1T sp. nov.

scholarly journals Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp.

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2666-2670 ◽  
Author(s):  
Xueqian Lei ◽  
Yi Li ◽  
Guanghua Wang ◽  
Yao Chen ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Biodiesel Production ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Rrna Gene Sequencing

A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3  % and pH from 5 to 9.Mg 2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5  % sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

scholarly journals Development and Evaluation of a PCR-Based Assay for Detection of Haemobartonella felis in Cats and Differentiation of H. felis from Related Bacteria by Restriction Fragment Length Polymorphism Analysis

1998 ◽  
Vol 36 (2) ◽  
pp. 462-466 ◽  
Author(s):  
Joanne B. Messick ◽  
Linda M. Berent ◽  
Sandra K. Cooper
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Mycoplasma Genitalium ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Doxycycline Treatment ◽  
Pcr Products ◽  
The 16S Rrna Gene

The 16S rRNA gene of Haemobartonella felis was amplified by using universal eubacterial primers and was subsequently cloned and sequenced. Based on this sequence data, we designed a set ofH. felis-specific primers. These primers selectively amplified a 1,316-bp DNA fragment of the 16S rRNA gene of H. felis from each of four experimentally infected cats at peak parasitemia. No PCR product was amplified from purified DNA ofEperythrozoon suis, Mycoplasma genitalium, andBartonella bacilliformis. Blood from the experimental cats prior to infection was negative for PCR products and was greatly diminished or absent 1 month after doxycycline treatment. The overall sequence identity of this fragment varied by less than 1.0% among experimentally infected cats. By taking into consideration the secondary structure of the 16S rRNA molecule, we were able to further verify the alignment of nucleotides and quality of our sequence data. In this PCR assay, the minimum detectable number of H. felis organisms was determined to be between 50 and 704. The potential usefulness of restriction enzymes DdeI andMnlI for distinguishing H. felis from closely related bacteria was examined. This is the first report of the utility of PCR-facilitated diagnosis and discrimination of H. felisinfection in cats.

scholarly journals Evaluation of recA Sequences for Identification of Mycobacterium Species

2000 ◽  
Vol 38 (8) ◽  
pp. 2846-2852 ◽  
Author(s):  
Kym S. Blackwood ◽  
Cheng He ◽  
James Gunton ◽  
Christine Y. Turenne ◽  
Joyce Wolfe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
Genetic Identification ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Accurate Identification

16S rRNA sequence data have been used to provide a molecular basis for an accurate system for identification of members of the genusMycobacterium. Previous studies have shown thatMycobacterium species demonstrate high levels (>94%) of 16S rRNA sequence similarity and that this method cannot differentiate between all species, i.e., M. gastri and M. kansasii. In the present study, we have used the recAgene as an alternative sequencing target in order to complement 16S rRNA sequence-based genetic identification. The recA genes of 30 Mycobacterium species were amplified by PCR, sequenced, and compared with the published recA sequences of M. tuberculosis, M. smegmatis, and M. leprae available from GenBank. By recA sequencing the species showed a lower degree of interspecies similarity than they did by 16S rRNA gene sequence analysis, ranging from 96.2% betweenM. gastri and M. kansasii to 75.7% betweenM. aurum and M. leprae. Exceptions to this were members of the M. tuberculosis complex, which were identical. Two strains of each of 27 species were tested, and the intraspecies similarity ranged from 98.7 to 100%. In addition, we identified new Mycobacterium species that contain a protein intron in their recA genes, similar to M. tuberculosis and M. leprae. We propose thatrecA gene sequencing offers a complementary method to 16S rRNA gene sequencing for the accurate identification of theMycobacterium species.

scholarly journals 16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene

1998 ◽  
Vol 36 (6) ◽  
pp. 1761-1764 ◽  
Author(s):  
U. Reischl ◽  
K. Feldmann ◽  
L. Naumann ◽  
B. J. M. Gaugler ◽  
B. Ninet ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Fragment Length Polymorphism ◽  
Direct Sequencing ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
The 16S Rrna Gene

Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

scholarly journals Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1784-1787 ◽  
Author(s):  
Hyunyoung Jeong ◽  
Young Woon Lim ◽  
Hana Yi ◽  
Yuji Sekiguchi ◽  
Yoichi Kamagata ◽  
...  
Keyword(s):  
16S Rrna ◽  
Forest Soil ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Phenotypic Characteristics ◽  
16S Rrna Sequence ◽  
Bacterium Strain ◽  
Low Levels

A strictly anaerobic, Gram-positive, endospore-forming bacterium, strain HY-37-4T, was isolated from a forest-soil sample collected in Jeju, Republic of Korea. The cells were motile rods with peritrichous flagella. Strain HY-37-4T fermented various carbohydrates and the end products from glucose were formate, acetate and H2. The major cellular fatty acids were C16 : 0, C16 : 0 3-OH and iso-C17 : 1 I/anteiso B. The G+C content of the DNA was 41 mol%. A phylogenetic analysis based on 16S rRNA sequence data indicated that the forest isolate was most closely related to Clostridium herbivorans, Clostridium populeti, Clostridium polysaccharolyticum and Eubacterium xylanophilum, which belong to Clostridium cluster XIVa. However, the low levels of 16S rRNA gene sequence similarity (92.3–93.9 %) with respect to these taxa indicate that strain HY-37-4T represents a novel species. Several phenotypic characteristics readily allowed the isolate to be distinguished from other phylogenetically related taxa. On the basis of the polyphasic evidence, strain HY-37-4T represents a novel taxon, for which the name Anaerosporobacter mobilis gen. nov., sp. nov. is proposed. The type strain is HY-37-4T (=IMSNU 40011T=KCTC 5027T=DSM 15930T).

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