16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity.

Snyder, Andrew R.; Williams, Henry N.; Baer, Marcie L.; Walker, Kimberly E.; Stine, O. Colin

doi:10.1099/00207713-52-6-2089

Cited by 27 publications

(31 citation statements)

References 16 publications

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“…The predatory, invasive, marine bacterium Bacteriovorax marinus is also closely related to B. bacteriovorus , although the Bdellovibrio and Bacteriovorax genera have diverged separately from Myxobacteria. A 16S rRNA phylogenetic tree of the deltaproteobacteria shows the ancestral lineage leading to Bdellovibrio and Bacteriovorax diverged from the ancestral lineage leading to the clade including Myxococcus xanthus [33] and in that divergent Bdellovibrio branch we detect mglB loss (Figure S1A). We found that in B. marinus , which also has an mglA gene (BMS_0054), there is an adjacent putative mglB homologue (BMS_0053), both genes lying downstream of recR (Figure S1B).…”

Section: Resultsmentioning

confidence: 95%

Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio

et al. 2014

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Bdellovibrio bacteriovorus invade Gram-negative bacteria in a predatory process requiring Type IV pili (T4P) at a single invasive pole, and also glide on surfaces to locate prey. Ras-like G-protein MglA, working with MglB and RomR in the deltaproteobacterium Myxococcus xanthus, regulates adventurous gliding and T4P-mediated social motility at both M. xanthus cell poles. Our bioinformatic analyses suggested that the GTPase activating protein (GAP)-encoding gene mglB was lost in Bdellovibrio, but critical residues for MglABd GTP-binding are conserved. Deletion of mglABd abolished prey-invasion, but not gliding, and reduced T4P formation. MglABd interacted with a previously uncharacterised tetratricopeptide repeat (TPR) domain protein Bd2492, which we show localises at the single invasive pole and is required for predation. Bd2492 and RomR also interacted with cyclic-di-GMP-binding receptor CdgA, required for rapid prey-invasion. Bd2492, RomRBd and CdgA localize to the invasive pole and may facilitate MglA-docking. Bd2492 was encoded from an operon encoding a TamAB-like secretion system. The TamA protein and RomR were found, by gene deletion tests, to be essential for viability in both predatory and non-predatory modes. Control proteins, which regulate bipolar T4P-mediated social motility in swarming groups of deltaproteobacteria, have adapted in evolution to regulate the anti-social process of unipolar prey-invasion in the “lone-hunter” Bdellovibrio. Thus GTP-binding proteins and cyclic-di-GMP inputs combine at a regulatory hub, turning on prey-invasion and allowing invasion and killing of bacterial pathogens and consequent predatory growth of Bdellovibrio.

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Section: Resultsmentioning

confidence: 95%

Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio

et al. 2014

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“…That a pure strain had been isolated was backed up by examination of restriction digest and Southern blot hybridisation patterns for DNA derived from multiple cultures of the Tiberius strain (data not shown) no variation was detected which would have indicated two strains rather than one. The 16SrRNA gene amplified from the genomic DNA of the Tiberius strain cultures gave a single uniform sequence which was used to position the bacterium on a phylogenetic tree (Additional file 1) where it clustered with Bdellovibrio bacteriovorus (rather than Bacteriovorax ) strains, including the type strain HD100 and the well-characterised lab strain 109J [12,13]. …”

Section: Resultsmentioning

confidence: 99%

“…This was repeated three times (each time selecting a single, well isolated plaque from the dilution plates) giving a culture that contained a single strain of Bdellovibrio preying upon the E. coli prey (Isolate Bdellovibrio bacteriovorus Tiberius isolate B5B). Purity was verified by microscopy, by consistency of SDS PAGE total protein patterns and by 16SrRNA PCR with both general-bacterial and Bdellovibrio -specific primers [12]. …”

Section: Methodsmentioning

confidence: 99%

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

et al. 2012

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BackgroundEvolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.ResultsTo test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.ConclusionsThe natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

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“…Bdellovibri o-and-like organisms (BALOs) are gram-negative, predatory bacteria that inhabit terrestrial, freshwater and saltwater environments and the intestinal tracts of animals and humans and, belong to the α - and δ -proteobacteria (Petrović-Gegić and Baloš, 2011; Taylor et al, 1974; Kelley and Williams, 1992; Snyder et al, 2002; Davidov and Jurkevitch, 2004, 2009; Chauhan and Williams, 2006). Most δ -proteobacteria BALO species, fall into two major genera, Bdellovibrio (BD) and Bacteriovorax (Bx) (Davidov and Jurkevitch, 2004; Chen et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms

Chen

Williams

2015

Gene

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Bdellovibrio -and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence–structure–function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations.

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16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity.

Cited by 27 publications

References 16 publications

Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio

Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio

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

Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms

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