scholarly journals Coexistence of Wolbachia with Buchnera aphidicola and a Secondary Symbiont in the Aphid Cinara cedri

2004 ◽  
Vol 186 (19) ◽  
pp. 6626-6633 ◽  
Author(s):  
Laura Gómez-Valero ◽  
Mario Soriano-Navarro ◽  
Vicente Pérez-Brocal ◽  
Abdelaziz Heddi ◽  
Andrés Moya ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Pcr Amplification ◽  
Bacterial Cells ◽  
Buchnera Aphidicola ◽  
Rdna Genes ◽  
16S Ribosomal Dna ◽  
Secondary Symbiont ◽  
Rdna Sequences ◽  
16S Rdna Sequences

ABSTRACT Intracellular symbiosis is very common in the insect world. For the aphid Cinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboring Buchnera aphidicola, the primary endosymbiont of aphids, C. cedri harbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an α-proteobacterium that belongs to the Wolbachia genus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA sequences, we have shown that Wolbachia was represented by only a few minute bacteria surrounding the S symbionts. Moreover, the observed B. aphidicola and the S symbionts had similar sizes and were housed in separate specific bacterial cells, the bacteriocytes. Interestingly, in contrast to the case for all aphids examined thus far, the S symbionts were shown to occupy a similarly sized or even larger bacteriocyte space than B. aphidicola. These findings, along with the facts that C. cedri harbors the B. aphidicola strain with the smallest bacterial genome and that the S symbionts infect all Cinara spp. analyzed so far, suggest the possibility of bacterial replacement in these species.

scholarly journals Niche-Partitioning of ProchlorococcusPopulations in a Stratified Water Column in the Eastern North Atlantic Ocean

1999 ◽  
Vol 65 (6) ◽  
pp. 2585-2591 ◽  
Author(s):  
Nyree J. West ◽  
David J. Scanlan
Keyword(s):  
Water Column ◽  
16S Rdna ◽  
North Atlantic ◽  
North Atlantic Ocean ◽  
Niche Partitioning ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Eastern North Atlantic ◽  
Eastern North Atlantic Ocean

ABSTRACT The in situ community structure of Prochlorococcuspopulations in the eastern North Atlantic Ocean was examined by analysis of Prochlorococcus 16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL) Prochlorococcus genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning ofProchlorococcus genotypes occurred. In each water column a shift from the HL to the LL genotype was observed, a transition correlating with the depth of the surface mixed layer (SML). Only the HL genotype was found in the SML in each water column, whereas the LL genotype was distributed below the SML. The range of in situ irradiance to which each genotype was subjected within these distinct niches was consistent with growth irradiance studies of cultured HL- and LL-adapted Prochlorococcus strains. DGGE analysis and the sequencing of Prochlorococcus 16S rDNA clones were in full agreement with the genotype-specific oligonucleotide probe hybridization data. These observations of a partitioning ofProchlorococcus genotypes in a stratified water column provide a genetic basis for the dim and brightProchlorococcus populations observed in flow cytometric signatures in several oceanic provinces.

scholarly journals Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the ε-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field

2004 ◽  
Vol 54 (1) ◽  
pp. 25-32 ◽  
Author(s):  
Ken Takai ◽  
Kenneth H. Nealson ◽  
Koki Horikoshi
Keyword(s):  
Thermophilic Bacterium ◽  
Black Smoker ◽  
Central Indian Ridge ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Group A ◽  
The Indian Ocean ◽  
Bacterium Strain ◽  
Indian Ridge

A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 °C (optimum temperature, 55 °C; 70 min doubling time) and between pH 4·9 and 7·2 (optimum, pH 5·9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated ε-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

Molecular phylogeny of some genera of Pamphagidae (Acridoidea, Orthoptera) from China based on mitochondrial 16S rDNA sequences

Zootaxa ◽  
2005 ◽  
Vol 1103 (1) ◽  
pp. 41 ◽  
Author(s):  
DAO-CHUAN ZHANG ◽  
XIN-JIANG LI ◽  
WEN-QIANG WANG ◽  
HONG YIN ◽  
ZHAN YIN ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
16S Rdna ◽  
Neighbor Joining ◽  
Minimum Evolution ◽  
Monophyletic Clade ◽  
16S Ribosomal Dna ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Phylogenetic Status ◽  
Nucleotide Divergence

Based on the mitochondrial 16S ribosomal DNA partial sequences (473 bp) of 9 species of Pamphagidae (Acridoidea, Orthoptera) from China and of 4 species of Pamphagidae and 2 species of Pyrgomorphidae and Acrididae (as outgroups) retrieved from GenBank, we constructed the molecular phylogeny using the Neighbor Joining (NJ) and Minimum Evolution (ME) methods based on the nucleotide Kimura 2-parameter model. The results of our study shown that: 1) the ranges of the 16S rDNA nucleotide divergence between two species of a genus were 0.21%, among genera of a subfamily were 0.42–3.38%, and among subfamilies of Pamphagidae were 1.90–8.88%, respectively. The phylogenetic tree shows that: 1) all Pamphagidae taxa form a monophyletic clade, and are well separated from the outgroup; 2) the African taxa Porthetinae (Lobosceliana brevicornis) and Akicerinae (Batrachotetrix sp.) are distinctly separated from the Chinese taxa Prionotropisinae; 3) Haplotropis bruneriana and Glauia terrea of Pamphaginae are nested in the middle of the tree, but their phylogenetic status is uncertain in this study; 4) 8 genera of Asiotmethis, Beybienkia, Mongolotmethis, Sinotmethis, Rhinotmethis, Filchnerella, Eotmethis and Pseudotmethis from China are all grouped into the subfamily Prionotropisinae, but their phylogenetic relationships are not clearly resolved.

scholarly journals In Situ Detection of Novel Bacterial Endosymbionts of Acanthamoeba spp. Phylogenetically Related to Members of the Order Rickettsiales

1999 ◽  
Vol 65 (1) ◽  
pp. 206-212 ◽  
Author(s):  
Thomas R. Fritsche ◽  
Matthias Horn ◽  
Seyedreza Seyedirashti ◽  
Romesh K. Gautom ◽  
Karl-Heinz Schleifer ◽  
...  
Keyword(s):  
16S Rdna ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Rrna Gene ◽  
Oligonucleotide Probes ◽  
Gram Negative ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Bacterial Endosymbionts

ABSTRACT Acanthamoebae are ubiquitous soil and water bactivores which may serve as amplification vehicles for a variety of pathogenic facultative bacteria and as hosts to other, presently uncultured bacterial endosymbionts. The spectrum of uncultured endosymbionts includes gram-negative rods and gram-variable cocci, the latter recently shown to be members of the Chlamydiales. We report here the isolation from corneal scrapings of two Acanthamoebastrains that harbor gram-negative rod endosymbionts that could not be cultured by standard techniques. These bacteria were phylogenetically characterized following amplification and sequencing of the near-full-length 16S rRNA gene. We used two fluorescently labelled oligonucleotide probes targeting signature regions within the retrieved sequences to detect these organisms in situ. Phylogenetic analyses demonstrated that they displayed 99.6% sequence similarity and formed an independent and well-separated lineage within theRickettsiales branch of the alpha subdivision of theProteobacteria. Nearest relatives included members of the genus Rickettsia, with sequence similarities of approximately 85 to 86%, suggesting that these symbionts are representatives of a new genus and, perhaps, family. Distance matrix, parsimony, and maximum-likelihood tree-generating methods all consistently supported deep branching of the 16S rDNA sequences within the Rickettsiales. The oligonucleotide probes displayed at least three mismatches to all other available 16S rDNA sequences, and they both readily permitted the unambiguous detection of rod-shaped bacteria within intact acanthamoebae by confocal laser-scanning microscopy. Considering the long-standing relationship of mostRickettsiales with arthropods, the finding of a related lineage of endosymbionts in protozoan hosts was unexpected and may have implications for the preadaptation and/or recruitment of rickettsia-like bacteria to metazoan hosts.

scholarly journals Secondary Intracellular Symbiotic Bacteria in Aphids of the GenusYamatocallis (Homoptera: Aphididae: Drepanosiphinae)

2001 ◽  
Vol 67 (11) ◽  
pp. 5315-5320 ◽  
Author(s):  
Takema Fukatsu
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Natural Populations ◽  
Symbiotic Bacterium ◽  
Nucleotide Substitution Rate ◽  
Diagnostic Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Phylogenetic

ABSTRACT A novel secondary intracellular symbiotic bacterium from aphids of the genus Yamatocallis (subfamily Drepanosiphinae) was characterized by using molecular phylogenetic analysis, in situ hybridization, and diagnostic PCR detection. In the aphid tissues, this bacterium (tentatively designated YSMS [Yamatocallis secondary mycetocyte symbiont]) was found specifically in large cells surrounded by primary mycetocytes harboringBuchnera cells. Of nine drepanosiphine aphids examined, YSMS was detected in only two species of the same genus,Yamatocallis tokyoensis and Yamatocallis hirayamae. In natural populations of these aphids, YSMS was present in 100% of the individuals. Phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences demonstrated that YSMS ofY. tokyoensis and Y. hirayamae constitute a distinct and isolated clade in the γ subdivision of the classProteobacteria. No 16S rDNA sequences of secondary endosymbionts characterized so far from other aphids showed phylogenetic affinity to YSMS. Based on these results, I suggest that YSMS was acquired by an ancestor of the genus Yamatocallisand has been conserved throughout the evolution of the lineage. By using the nucleotide substitution rate for 16S rDNA ofBuchnera spp., the time of acquisition of YSMS was estimated to be about 13 to 26 million years ago, in the Miocene epoch of the Tertiary period.

scholarly journals Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization

2007 ◽  
Vol 73 (7) ◽  
pp. 2324-2328 ◽  
Author(s):  
Irina Smolina ◽  
Charles Lee ◽  
Maxim Frank-Kamenetskii
Keyword(s):  
Dna Sequences ◽  
Peptide Nucleic Acid ◽  
Rolling Circle Amplification ◽  
Bacterial Genome ◽  
Bacterial Cells ◽  
Rolling Circle ◽  
Low Copy Number ◽  
Short Signature ◽  
In Situ Detection

ABSTRACT An approach is proposed for in situ detection of short signature DNA sequences present in single copies per bacterial genome. The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes.

Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)

1998 ◽  
Vol 64 (10) ◽  
pp. 3599-3606 ◽  
Author(s):  
Takema Fukatsu ◽  
Naruo Nikoh
Keyword(s):  
In Situ Hybridization ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Symbiotic Bacteria ◽  
Polymorphism Analysis ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Phylogenetic

ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA ofA. mori, and two clones, the A-type and B-type clones, were identified by restriction fragment length polymorphism analysis. In situ hybridization with specific oligonucleotide probes demonstrated that the A-type and B-type 16S rDNAs were derived from the X-symbionts and Y-symbionts, respectively. Molecular phylogenetic analyses of the 16S rDNA sequences showed that these symbionts belong to distinct lineages in the γ subdivision of the Proteobacteria. No 16S rDNA sequences in the databases were closely related to the 16S rDNA sequences of the X- and Y-symbionts. However, the sequences that were relatively closely related to them were the sequences of endosymbionts of other insects. The nucleotide compositions of the 16S rDNAs of the X- and Y-symbionts were highly AT biased, and the sequence of the X-symbiont was the most AT-rich bacterial 16S rDNA sequence reported so far.

scholarly journals Bacterial DNA Diversity among Clear and Cloudy Sakes, and Sake-kasu

2020 ◽  
Vol 13 (1) ◽  
pp. 74-82
Author(s):  
Momoka Terasaki ◽  
Hiromi Nishida
Keyword(s):  
Production Process ◽  
Dna Sequences ◽  
Bacterial Contamination ◽  
Yeast Cells ◽  
Bacterial Cells ◽  
Bacterial Dna ◽  
Rdna Sequences ◽  
Dna Diversity ◽  
16S Rdna Sequences ◽  
The Difference

Background: The traditional Japanese alcoholic drink, sake, is classified into two types: those that contain sediment produced during the production process (cloudy sakes) and those that do not contain such sediment (clear sakes). Leftover pressed sediment from the sake production process, sake-kasu (sake cake or sake lees), is commercially available and is highly nutritious for humans. Objective: The purpose of this study was to determine the difference among component bacterial DNA sequences of clear and cloudy sakes, and sake-kasu. Methods: We compared the 16S rDNA sequences from 44 samples of clear sake, 3 samples of cloudy sake, and 11 samples of sake-kasu. Results: The DNA sequences were divided into three major clusters; however, sequences in sake-kasu were located in just one cluster forming two lineages. The microbial diversity in sake-kasu was lower than that in clear and cloudy sakes, which may be because some of the contaminating bacterial cells do not lyse during the production process and remain intact, along with yeast cells, in sake-kasu. Conclusion: Bacterial DNA frequently detected in sake samples was from environmental bacterial contamination that occurs early in the sake production process. Contaminating bacteria are usually killed by the ethanol produced as the sake yeast grows; after which, if bacteria lyse, the bacterial DNA is released into the sake solution. However, if the bacterial cells do not lyse, they will precipitate toward the sediment. Thus, there is bacterial DNA diversity in clear and cloudy sake, but less diversity in sake-kasu.

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