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 Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

scholarly journals Campylobacter fetus subspecies fetus spondylodiscitis

2010 ◽  
Vol 59 (12) ◽  
pp. 1505-1508 ◽  
Author(s):  
Antoine Chaillon ◽  
Gaelle Baty ◽  
Marie Agnès Lauvin ◽  
Jean Marc Besnier ◽  
Alain Goudeau ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rrna Gene ◽  
Gastrointestinal Infections ◽  
Systemic Complications ◽  
Campylobacter Fetus ◽  
Common Causes ◽  
Vertebral Biopsy ◽  
The 16S Rrna Gene ◽  
Predisposing Conditions

Campylobacter spp. are common causes of gastrointestinal infections. Campylobacter fetus is a much rarer pathogen in humans, and usually causes bacteraemia and systemic complications in patients with predisposing conditions. We report a case of spondylodiscitis caused by C. fetus subsp. fetus as revealed by vertebral biopsy culture. This identification was confirmed by sequencing the 16S rRNA gene and by phylogenetic analysis. Treatment consisted of 6 weeks antimicrobial therapy combined with a strict initial immobilization, followed by a re-education program. The patient's recovery was uneventful.

scholarly journals Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK

2007 ◽  
Vol 57 (2) ◽  
pp. 276-286 ◽  
Author(s):  
Ivo M. Chelo ◽  
Líbia Zé-Zé ◽  
Rogério Tenreiro
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Phylogenetic Structure ◽  
The 16S Rrna Gene ◽  
Combined Data ◽  
Good Agreement

The phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.

scholarly journals MOLECULAR CHARACTERIZATION OF GENE 16S rRNA MICRO SYMBIONTS IN SPONGE AT MELAWAI BEACH, EAST KALIMANTAN

2018 ◽  
Author(s):  
Ismail Marzuki ◽  
Alfian Noor ◽  
Nursiah La Nafie
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Isolation And Purification ◽  
East Kalimantan ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

Molecular characterization studies have been conducted 16S rRNA gene micro symbiont of sponge origin Melawai Beach, Balikpapan in East Kalimantan. Objective analysis of histo- morphological research, isolation-purification, molecular characterization of micro-symbiont genes in order to search symbiont bacteria that can live in extreme environments contaminated hydrocarbon waste. The research method that morphological identification, isolation-purification and molecular characterization of the 16S rRNA gene with Chain Reaction Polymerization method. The results of histo-morphological analysis concluded sponge samples with species of Callyspongia sp. Isolation and purification mikro symbionts of sponge obtained 2 (two) isolates. Characteristics of Isolates 1; spherical shape, colonize and creamy, while isolates 2; jagged shape, oval and white colonies. Molecular characterization of the 16S rRNA gene by PCR, Bacillus subtilis strain BAB-684 identification for isolates one is the number of nucleotide pairs reached 899 bp and the degree of similarity in GenBank reached 89% homologous, while the second is a Bacillus flexus strain PHCDB20 isolates the number reached 950 bp nucleotide pairs with the degree of similarity in GenBank reached 99% homologous

scholarly journals Identification and characterization of Flavobacteriaceae from farmed Oreochromis niloticus and Clarius gariepinus in Uganda

2018 ◽  
Vol 8 (1) ◽  
pp. 42-50
Author(s):  
AMONO RACHEAL ◽  
CHRISTOPHER J. KASANGA ◽  
DENIS K. BYARUGABA
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Oreochromis Niloticus ◽  
Control Measure ◽  
African Catfish ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Identification And Characterization

Racheal A, Kasanga CJ, Byarugaba DK. 2018. Identification and characterization of Flavobacteriaceae from farmed Oreochromis niloticusand Clarius garieoinus. Bonorowo Wetlands 2: 42-50. Bacteria under family Flavobacteriaceae (in this study were also referred to as Flavobacteria) are important pathogens of fish, people, many other animals and plants. In this study, Flavobacteria from Nile tilapia (Oreochromis niloticus) and African catfish (Clarius gariepinus) were identified and characterized from the selected farms in Uganda. Gill and skin swabs were obtained from a total of 119 fish from 19 farms and were dissected aseptically to sample internal organs. The samples were inoculated onto Sheih media and incubated at 25°C for 48 hours. The suspected isolates were identified by colon characteristics, conventional biochemical tests and API 20 NE kits. The isolates were grouped into eight based on colon characteristic similarity. One isolate was selected per group for 16S rRNA gene sequencing and identified using the EZbiocloud.net ID software. Phylogenetic analysis of selected isolates was performed using the 16S rRNA gene sequences in BioEdit and MEGA 7.0.2 software. Basing on extrapolation of sequence analysis of the selected isolates, out of the 86 isolates, Myroides marinus was the most predominant species taking up 4 of the 8 groups (60 isolates) in 13 farms. The rest of the groups comprised of; Acinetobacter pitti, one group (6 isolates) in 6 farms, Chryseobacterium gambrini 2 groups (3 isolates) in 3 farms and one isolate was unidentified, in 3 farms. However, a total of 16 isolates did not grow on sub culturing. Phylogenetic analysis indicated that M. marinus isolates grouped with other M. marinus isolates from gene bank with significant intra-species diversity which was also observed with C. gambrini isolates. All the sampled farms had at least one isolate of a Flavobacterium from Tilapia and/or Catfish. Pathogenicity studies should be conducted on the isolates to establish their importance as fish pathogens and transmission dynamics so that an appropriate control measure can be recommended.

‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 636-640 ◽  
Author(s):  
Nang Kyu Kyu Win ◽  
Seung-Yeol Lee ◽  
Assunta Bertaccini ◽  
Shigetou Namba ◽  
Hee-Young Jung
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus Phytoplasma ulmi ’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region differentiated the BltWB phytoplasma from ‘Ca. P. ziziphi ’, ‘Ca. P. ulmi ’ and ‘Candidatus Phytoplasma trifolii ’. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other ‘Candidatus Phytoplasma ’ taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, ‘Candidatus Phytoplasma balanitae’.

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