Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of Two<i>Bdellovibrio</i>Species Isolated from Soil

Oyedara, Omotayo Opemipo; Segura‐Cabrera, Aldo; Guo, Xianwu; Elufisan, Temidayo Oluyomi; González, Rafael Alejandro Cantú; Pérez, Mario A. Rodríguez

doi:10.1155/2018/9402073

Cited by 11 publications

(7 citation statements)

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“…We compared the core genome defined by our analysis with the set of 795 conserved Bdellovibrio genes identified in [23]. To do this, we extracted NCBI protein accession numbers associated with B. exovorus JSS from Additional File 4a, because JSS was the only genome for which all 795 genes were listed.…”

Section: Comparative Genomics Of Bdellovibrio Sp Nc01 and Other Sequmentioning

confidence: 99%

“…Recently, Oyedara and colleagues conducted comparative genomics of the same six publicly available complete Bdellovibrio genomes and the genome of Bdellovibrio sp. SKB1291214, which is not complete [23]. The core genome shared by these seven Bdellovibrio strains included 795 protein-coding genes.…”

Section: Analysis Of Orthologue Groups Identifies Proteincoding Genesmentioning

confidence: 99%

“…Currently, only a few completely sequenced predatory bacteria genomes are available in public databases. In addition to HD100, there are only four other completely sequenced intraperiplasmic Bdellovibrio genomes, including B. bacteriovorus W [22], which is the most phylogenetically divergent from HD100 [23]. The limited genome dataset highlights the importance of sequencing additional Bdellovibrio, especially strains that are divergent from HD100.…”

Section: Introductionmentioning

confidence: 99%

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Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100

et al. 2019

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Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four proteincoding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.

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Section: Comparative Genomics Of Bdellovibrio Sp Nc01 and Other Sequmentioning

confidence: 99%

Section: Analysis Of Orthologue Groups Identifies Proteincoding Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100

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“…We clustered amino acid sequences from NC01, all five publicly available completely sequenced Bdellovibrio bacteriovorus , and Bdellovibrio exovorus JSS into ortholog groups. We then compared our analysis with a previous analysis of conserved protein-coding genes reported in (23), which included the same six publicly available Bdellovibrio genomes and an additional partially sequenced genome of a Bdellovibrio strain isolated from soil. This comparison identified 778 protein-coding genes conserved among all eight Bdellovibrio genomes.…”

Section: Discussionmentioning

confidence: 99%

Variation in genome content and predatory phenotypes betweenBdellovibriosp. NC01 isolated from soil andB. bacteriovorustype strain HD100

Williams

Cullen

DeGiorgis

et al. 2019

Preprint

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13Defining phenotypic and associated genotypic variation among Bdellovibrio may further 14 our understanding of how this genus attacks and kills different Gram-negative bacteria. We 15 isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average 16 amino acid identity showed that NC01 belongs to a different species than the type species 17 bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and 18 comparing the resulting ortholog groups to a previously published analysis, we defined a "core 19 genome" of 778 protein-coding genes and identified four protein-coding genes that appeared to 20 be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted 21 NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide 22 sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To 23 investigate how genome variation may impact predation, we compared protein-coding gene 24 content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes 25 implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that 26 may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested 27 prey strains and kills E. coli ML35 less efficiently. NC01 causes a smaller log reduction in 28 ML35, after which the prey population recovers and the NC01 population decreases. In addition, 29 NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by 30 HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative 31 bacteria with underlying Bdellovibrio genome variation is valuable for understanding the 32 ecological significance of predatory bacteria and evaluating their effectiveness in clinical 33 applications.34 35Since their discovery in the early 1960s, predatory bacteria have been isolated from a 36 wide range of terrestrial and aquatic environments, including some with extreme conditions such 37 as high temperature or salinity (1). The impact of predatory bacteria in these environments is not 38 fully known, but recent studies indicate they may play an important role in shaping microbial 39 communities (2-4). In addition, their ability to attack and kill Gram-negative bacterial pathogens 40 has generated interest in developing predatory bacteria as biocontrol agents to combat drug-41 resistant infections (5-7). Given their potential ecological significance and possible clinical 42 applications, it is important to define phenotypic and genotypic variation among predatory 43 bacteria. In particular, variation in predatory phenotypes such as prey range and predation 44 efficiency will affect how different strains of predatory bacteria impact microbial communities, 45 and this phenotypic variation may be determined by variation in genome content. To further our 46 understanding of phenotypic and genome variation in predatory bacteria, we isolated, assayed 4...

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“…Genome sequencing has been used to explain detailed characteristics of many bacteria including their metabolic behavior (Makarova et al, 2001;Oyedara et al, 2018). Genome sequencing of some bacteria with the potentials to degrade hydrocarbons and PAHs has given profound insight into the genes involved in the degradation and mineralization of PAHs (Gunsalus, 1951;Schneiker et al, 2006;Kim et al, 2008, Das & Chandran, 2011Pal et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico

Elufisan

Rodríguez-Luna

Oyedara

et al. 2020

PeerJ

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Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.

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Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of TwoBdellovibrioSpecies Isolated from Soil

Cited by 11 publications

References 46 publications

Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100

Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100

Variation in genome content and predatory phenotypes betweenBdellovibriosp. NC01 isolated from soil andB. bacteriovorustype strain HD100

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico

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