scholarly journals Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice

2015 ◽  
Author(s):  
Julie M Allen ◽  
J Gordon Burleigh ◽  
Jessica E Light ◽  
David L Reed
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Sampling Strategies ◽  
Host Group ◽  
Rdna Sequences ◽  
Endosymbiotic Bacteria ◽  
16S Rdna Sequences ◽  
Evolutionary Inference ◽  
Sucking Lice ◽  
Diversity Sampling

Co-evolution between insects and their endosymbiotic bacteria can be detected by constructing and comparing their phylogenetic trees. Even though taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships and estimates of the number of endosymbiont lineages within a host group have used only a small percentage of available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. We found that sampling of 16S rDNA sequences affected the estimates of endosymbiont diversity in sucking lice until we reached a threshold of genetic diversity. Sampling by maximizing the diversity of 16S rDNA sequences was more efficient than simply randomly sampling available 16S rDNA sequences. Although simulation results support the finding of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that there is still uncertainty in estimates of the number of endosymbiont origins inferred from 16S rDNA alone.

scholarly journals Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice

2015 ◽  
Author(s):  
Julie M Allen ◽  
J Gordon Burleigh ◽  
Jessica E Light ◽  
David L Reed
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Sampling Strategies ◽  
Host Group ◽  
Rdna Sequences ◽  
Endosymbiotic Bacteria ◽  
16S Rdna Sequences ◽  
Evolutionary Inference ◽  
Sucking Lice ◽  
Diversity Sampling

Co-evolution between insects and their endosymbiotic bacteria can be detected by constructing and comparing their phylogenetic trees. Even though taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships and estimates of the number of endosymbiont lineages within a host group have used only a small percentage of available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. We found that sampling of 16S rDNA sequences affected the estimates of endosymbiont diversity in sucking lice until we reached a threshold of genetic diversity. Sampling by maximizing the diversity of 16S rDNA sequences was more efficient than simply randomly sampling available 16S rDNA sequences. Although simulation results support the finding of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that there is still uncertainty in estimates of the number of endosymbiont origins inferred from 16S rDNA alone.

scholarly journals Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2187 ◽  
Author(s):  
Julie M. Allen ◽  
J. Gordon Burleigh ◽  
Jessica E. Light ◽  
David L. Reed
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Sampling Strategy ◽  
Taxon Sampling ◽  
Sampling Strategies ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Evolutionary Inference ◽  
Sucking Lice ◽  
Simulation Results

Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies ofGammaproteobacteriasequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from otherGammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.

Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3423 (1) ◽  
pp. 61 ◽  
Author(s):  
JERZY A. LIS ◽  
PAWEŁ LIS ◽  
DARIUSZ J. ZIAJA ◽  
ANNA KOCOREK
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Sister Group ◽  
Systematic Position ◽  
Bayesian Phylogenetic Analysis ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Affinity ◽  
The Moment

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous morphological analyses that placed it within the subfamily Megymeninae. We suggest restoring taxonomic status of the tribe Eumenotini and removing it from the synonymy of Megymenini, leaving the genus with no subfamilial assignment for the moment.

Phylogenetic placement of unculturedCeanothusmicrosymbionts using 16S rRNA gene sequences

1999 ◽  
Vol 77 (9) ◽  
pp. 1208-1213 ◽  
Author(s):  
Nancy J Ritchie ◽  
David D Myrold
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Full Length ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Polymerase Chain ◽  
Ceanothus Americanus

Full-length 16S rDNA sequences were amplified directly from the nodules of Ceanothus americanus L. and Ceanothus thyrsiflorus Eschsch. using the polymerase chain reaction. Sequences were determined using an automated sequencer, compared against those in GenBank, and assembled into consensus sequences. The sequences were aligned with other full-length Frankia 16S rDNA sequences available from the data base. Phylogenetic trees were obtained using three different algorithms: neighbor joining, parsimony, and the maximum-likelihood method. All three methods showed that these Ceanothus L. microsymbionts were most closely related to the microsymbiont associated with Dryas drummondii Richardson ex Hook. Lvs. rather than Frankia isolated from the Elaeagnaceae.Key words: Frankia, Ceanothus, 16S rDNA.

scholarly journals Isolation and Detection of Bacteriocin-Like Inhibitory Substances-Producing Bacteria from Fermented Mare’s Milk Sumbawa

2019 ◽  
Vol 4 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Alifia Issabella Mulyawati ◽  
Tri Ardyati ◽  
Yoga Dwi Jatmiko
Keyword(s):  
Antibacterial Activity ◽  
16S Rdna ◽  
Broad Spectrum ◽  
Phylogenetic Trees ◽  
Pathogenic Bacteria ◽  
Lactobacillus Rhamnosus ◽  
Proteinase K ◽  
Bacterial Strains ◽  
Rdna Sequences ◽  
16S Rdna Sequences

  Bacteriocin-like inhibitory substances (BLIS) produced by bacteria is a promising future food preservative agent. This study aimed to obtain bacterial strains that can produce broad-spectrum antibacterial agents and identify the best BLIS producer species based on 16S rDNA sequences. The bacterial strains were isolated from fer-mented mare’s milk using MRS and M17 agar medium. The isolates then were initially screened based on its antibacterial activity of crude cells against Staphylococcus aureus ATCC 6538. The selected strains were cultured and harvested for its cell-free supernatant (CFS). The pH of CFS was adjusted to 6.5 then used for antibacterial activity as-says against ten pathogenic bacteria. Also, the proteinaceous nature of BLIS compound was confirmed by testing with proteinase K. The gDNA of selected isolates was extracted and the 16S rDNA was am-plified using the polymerase chain reaction method then sequenced. The 16S rDNA sequences of the selected strains were used to identify the species using BLAST nucleotides from NCBI then the phylogenetic trees were constructed. 32 isolates was obtained, but only three iso-lates (BC9, SB7, and DC12) were selected as a result of antibacterial screening for further assays. The neutralized-CFS (N-CFS) of these isolates exhibited broad-spectrum antibacterial activity. The N-CFS could be assumed as BLIS. The isolate of BC9 was identified as Ba-cillus amyloliquefaciens strain BC9 that has 99.99 % similarity with B. amyloliquefaciens KC-1, SB7 was Lactobacillus plantarum strain SB7 that has 99.99 % similarity with Lb. plantarum JMC 1149T, and DC12 was Lactobacillus rhamnosus strain DC12 that has 100 % sim-ilarity with Lb. rhamnosus DSM 20021T. Thus, the BLIS produced by those strains is potential for future food and beverages preservations. 

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

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