Colony PCR Amplification of Actinomycete DNA

Gathogo, Esther; Waugh, Amy; Perić, Nataša; Redpath, Maria B.; Long, Paul F.

doi:10.7164/antibiotics.56.423

Cited by 19 publications

(8 citation statements)

References 3 publications

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“…A colony PCR method was used for the amplification of 16S rRNA gene fragments (Gathogo et al 2003). PCR was performed with the primers 27f and 1492r (Lane 1991).…”

Section: Methodsmentioning

confidence: 99%

Plasmid diversity in arctic strains of Psychrobacter spp.

et al. 2013

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Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)—an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments.Electronic supplementary materialThe online version of this article (doi:10.1007/s00792-013-0521-0) contains supplementary material, which is available to authorized users.

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“…A colony PCR method was used for the amplification of 16S rRNA gene fragments (Gathogo et al 2003). PCR was performed with the primers 27f and 1492r (Lane 1991).…”

Section: Methodsmentioning

confidence: 99%

Plasmid diversity in arctic strains of Psychrobacter spp.

et al. 2013

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“…The sacB- specific primers used to identify the target site of transposition, were previously described by Szuplewska and Bartosik [20]. A colony PCR method for the amplification of 16S rRNA genes [28], used primers 27f and 1492r [29]. The transformation of E. coli strains was performed according to the method of Kushner [30].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

et al. 2013

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BackgroundHalomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.ResultsThe analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.ConclusionsThis study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.

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“…Isolates were identified using molecular sequencing method [26] . The QIAGEN HotStarTaq ® Multiplex PCR Kit and the primers B27F and 1492R were used to obtain PCR products, which were subsequently were sequenced at Macrogen Inc. (South Korea, http://www.macrogen.com/ ).…”

Section: Methodsmentioning

confidence: 99%

Streptophage-mediated control of off-flavour taint producing streptomycetes isolated from barramundi ponds

Jonns

Brooks

Exley

et al. 2017

Synthetic and Systems Biotechnology

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Off-flavour taint of aquaculture products is a global issue reducing consumer confidence in the farmed produce as they are taken up via the gills of fish, and deposited in the lipids of the animal. If the fish are not purged, resulting undesirable muddy earthy flavour taint can be tasted by consumers. These undesirable flavour and odour is caused by the terpenoid compounds namely geosmin and 2-methylisoborneol, produced as secondary metabolites by certain bacteria including the cyanobacteria and actinomycetes. Current strategies to remediate the problem rely on treating the symptoms not the cause and involve the use of time consuming purging methods and costly chemicals.Biological control using bacteriophages, specific to the problem causing bacteria, offers a natural alternative to chemical control, which might reduce further complications of copper based algaecides and its subsequent implications on water quality. In an adaptation of such biological control approach streptomycetes isolated from barramundi ponds were tested for their susceptibility to streptophages to understand whether host destruction via phage lysis would subsequently eliminate off-flavour taint productions by these isolates.Following the determination of the streptophage susceptibility of the isolates one of the most odourous streptomycete species (USC-14510) was selected to be tested further using different pond simulations resembling real-life applications. Geosmin was tested as the indicator of off-flavour taint production and as it has been previously reported that the cyanobacteria-actinomycete interactions occurring in ponds result in even greater levels of geosmin and 2-methylisoborneol, the geosmin levels for the isolate in the presence of cyanobacteria and streptophages were also tested. Findings indicated that the highly odourous Streptomyces species (USC-14510) once infected with streptophages, can lose its capacity to produce off-flavour taints. Pond simulation studies also revealed geosmin production was significantly reduced when streptophages were introduced into the pond water where streptomycete species were grown. The bacteriophage control method developed in the presented study might again confirm significant potential for the bacteriophage-mediated remediation strategy to be adapted by the aquaculture industry.

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Colony PCR Amplification of Actinomycete DNA

Cited by 19 publications

References 3 publications

Plasmid diversity in arctic strains of Psychrobacter spp.

Plasmid diversity in arctic strains of Psychrobacter spp.

Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

Streptophage-mediated control of off-flavour taint producing streptomycetes isolated from barramundi ponds

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