Open Access Research article

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

Laura Hobley13, Thomas R Lerner14, Laura E Williams2, Carey Lambert1, Rob Till1, David S Milner1, Sarah M Basford1, Michael J Capeness1, Andrew K Fenton15, Robert J Atterbury16, Maximilian ATS Harris1 and R Elizabeth Sockett1*

Author Affiliations

1 Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School QMC, Derby Road, Nottingham, NG7 2UH, UK

2 Institute for Genome Sciences and Policy, Duke University, Durham, NC, 27708, USA

3 Current addresses: College of Life Sciences, University of Dundee, Dow Street, Dundee, Scotland, DD1 5EH, UK

4 Current addresses: Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK

5 Current addresses: Centre for Bacterial Cell Biology, University of Newcastle, Newcastle Upon Tyne, NE2 4AX, UK

6 School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK

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BMC Genomics 2012, 13:670  doi:10.1186/1471-2164-13-670

Published: 27 November 2012

Additional files

Additional file 1:

Phylogentic tree of theBdellovibrionalesincludingB. bacteriovorusTiberius. Neighbour-joining tree of the 16S rRNA sequences of the Bdellovibrionales. B. bacteriovorus Tiberius is shown by its isolate number ‘b5b’. Tree produced using the in-built neighbour-joining algorithms in the Arb program, and bootstrapped using n=500. Myxococcus xanthus Mx1622 was used as an outgroup to root the tree.

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Additional file 2:

Stills from timelapse microscopy video showing simultaneous growth and division of B. bacteriovorus Tiberius: A filamentous B. bacteriovorus Tiberius grows, divides and fragments in a large E.coli prey bdelloplast (lower arrow) while a smaller B. bacteriovorus Tiberius (upper arrow) elongates prey-independently. Shown by time lapse microscopy from a predator-prey culture in calcium-HEPES buffer, supported on an agarose pad on a microscope slide.

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Additional file 3:

Graph showing B. bacteriovorus Tiberius host-independent growth of cells from a predatorily grown culture: Spontaneously streptomycin-resistant Tiberius cells were taken directly from a culture grown on prey cells. They were then directly grown in PY broth (Horowitz et al., 1974) in the presence of streptomycin to inhibit growth of prey E. coli (still present in the co-culture). The resulting Tiberius growth was measured as an increase in OD at 600 nm, shown in the graph against time of incubation at 29°C. The larger prey-independent cells of Tiberius were large enough to measure by optical density (although attack phase sized Bdellovibrio are not) , thus the OD600nm values are probably an under-estimate of the growth rate of total Bdellovibrio (including smaller cells) in the population. The data shown are from 3 independent repeats and the error bars are 1 standard deviation from the mean.

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Additional file 4:

Graph showing evidence of killing of E. coli S17-1 and growth of B. bacteriovorus Tiberius in a predatory culture. Start- and end-point analyses of viable cell numbers of E. coli prey cells and Tiberius predatory cells by plaque (Tiberius) and colony (E. coli) counts on soft agar overlays on prey lawns, or conventional LB agar plates, respectively.

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Additional file 5:

ACT comparison of B. bacteriovorus HD100 and Tiberius genomes. HD100 is shown along the top of the comparison, with Tiberius below. Areas shown in red are regions of high synteny; blue lines represent areas of homology but in reverse orientation.

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Additional file 6:

Unique Genes called by RSD and by Manual Blast. First page shows the annotation of all genes in each of the HD100 and Tiberius genomes alongside whether they were identified as being unique by either RSD or blast analyses. Second page shows only those genes identified as unique by either analysis method, listed by Bd# or Bdt#. The third page again shows the unique genes, this time listed by analysis method.

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Additional file 7:

Evolutionary rates analysis for all 3203 orthologous genes in B. bacteriovorus HD100 and Tiberius predicted by RSD. Substitution rates were estimated by pairwise comparison in PAML. Red highlighting denotes pairs with dS > 1.5, which indicates saturation of synonymous sites. Table title headings are as follows: ortholog pair (from RSD) = this is a code assigned by our in-house scripts; sites = number of nucleotides (minus the stop codon); dN = average number of nonsynonymous changes per nonsynonymous site; dNse = standard error of dN (calculated by the curvature method); dS = average number of synonymous changes per synonymous site; dSse = standard error of dS (calculated by the curvature method); lnL = likelihood of the evolutionary model used in PAML analysis; t = sequence distance estimated by maximum likelihood; kappa = estimated transition/transversion rate ratio; omega = dN/dS.

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Additional file 8:

Table showing the location and composition of unique gene islands located next to tRNAs.

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Additional file 9:

a. DNA encoding ICE like transposase element, 6 identical insertions of which were unique to the B. bacteriovorus Tiberius genome.b. predicted domains on encoded protein from Blast X search. c. Alignment of Tiberius encoded IS element product translated from bases 7–732 with insertion element IS2 transposase catalytic protein InsD of E.coli. The amino-acid sequences are 48% identical.

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Additional file 10:

Table showing the location and type of each tRNA identified by tRNAScan-SE in the genomes of B. bacteriovorus HD100 and Tiberius. Note the absence of the Pro-type tRNA from the Tiberius genome.

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