Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip Sites

Yang, Yiren; Yu, Xuefei; Zhang, Ren

doi:10.1128/genomea.00173-13

Cited by 12 publications

(8 citation statements)

References 6 publications

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“…Diverse Ochrobactrum sps. have been reported from contaminated habitat which showed its role in bioremediation and tolerance to different heavy metals like Arsenic, Nicotine [7] , [8] and were found in earlier as well as resequenced strain. In addition, presence of genes coding for Arsenic ( ArsH , Acr3 , Arsenate reductase ) Copper ( CutE , CcmH , CopC , CopD , Copper chaperone , CopG , CcmM , Copper-translocating P-type ATPase , Blue copper oxidase CueO precursor ), Cobalt-zinc-cadmium resistance ( Co / Zn / Cd efflux system membrane fusion protein ) and Mercuric reductase were also detected in earlier and resequenced strain indicating the necessity of these genes for growth under in-vitro as well as in-vivo environment.…”

Section: Resultsmentioning

confidence: 96%

Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions

et al. 2016

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Advances in de novo sequencing technologies allow us to track deeper insights into microbial genomes for restructuring events during the course of their evolution inside and outside the host. Bacterial species belonging to Ochrobactrum genus are being reported as emerging, and opportunistic pathogens in this technology driven era probably due to insertion and deletion of genes. The Ochrobactrumintermedium M86 was isolated in 2005 from a case of non-ulcer dyspeptic human stomach followed by its first draft genome sequence in 2009. Here we report re-sequencing of O. intermedium M86 laboratory adapted strain in terms of gain and loss of genes. We also attempted for finer scale genome sequence with 10 times more genome coverage than earlier one followed by comparative evaluation on Ion PGM and Illumina MiSeq. Despite their similarities at genomic level, lab-adapted strain mainly lacked genes encoding for transposase protein, insertion elements family, phage tail-proteins that were not detected in original strain on both chromosomes. Interestingly, a 5 kb indel was detected in chromosome 2 that was absent in original strain mapped with phage integrase gene of Rhizobium spp. and may be acquired and integrated through horizontal gene transfer indicating the gene loss and gene gain phenomenon in this genus. Majority of indel fragments did not match with known genes indicating more bioinformatic dissection of this fragment. Additionally we report genes related to antibiotic resistance, heavy metal tolerance in earlier and re-sequenced strain. Though SNPs detected, there did not span urease and flagellar genes. We also conclude that third generation sequencing technologies might be useful for understanding genomic architecture and re-arrangement of genes in the genome due to their ability of larger coverage that can be used to trace evolutionary aspects in microbial system.

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Section: Resultsmentioning

confidence: 96%

Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions

et al. 2016

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“…Those strains were tolerant to heavy metals as lead, nickel, copper and arsenic. In bioremediation, the use of resistant strains offers many perspectives because the ability of telluric microorganisms to interact with plants allows the combination of bioremediation and phytoremediation process [29,30].…”

Section: Discussionmentioning

confidence: 99%

Isolation and Identification of Heavy Metals and Antibiotics Resistant Strains from Antananarivo Dumpsite, Madagascar

Andriamafana¹,

Mong²,

Onja³

et al. 2018

IJMB

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Heavy metals contamination is now widespread in the nature. At higher concentration, heavy metals become toxic and disturb the ecosystem including soil microorganisms. To adapt to such constraints, some microorganisms have developed tolerance mechanisms. Indeed, in the environment, the resistance of microorganisms to heavy metal often promotes to antibiotic resistance. This work aims to isolate strains from soil samples collected in Andralanitra landfill, to test their tolerance to heavy metals, to identify tolerant strains and to verify their resistance to antibiotics. According to the dilution method, a total of 48 strains were obtained, 14 were isolated on PDA medium, 10 on Sabouraud agar medium, 10 strains on Mossel agar medium, 7 on AS1 medium, 5 strains on TSA medium and 2 strains with King B medium. Resistance test to heavy metals performed by the wells method showed that out of the 48 isolated strains, 26 were capable to grow in the presence of heavy metals (solution composed of copper, zinc, cadmium, chromium, nickel, lead) at different concentrations. The highest number of tolerant strains was recorded at the concentration of 100mg/L ≤ C ≤ 1000mg/L. Four (4) strains were tolerant to the heavy metals solution at a concentration between 100mg/L and 1500mg/L. The molecular identification of these four most resistant strains by 16S rDNA gene sequencing and ITS gene sequencing allowed to classify them as belonging to the genera Ochrobactrum pseudogrignonense, Arthrobacter nicotianae, Penicillium crustosum and Penicillium commune. The antibiotic sensitivity test using disc diffusion method on Mueller-Hinton agar revealed that Ochrobactrum pseudogrignonense and Penicillium commune were resistant to Trimethoprim, Arthrobacter nicotianae showed resistance to Trimethoprim and Ciprofloxacin, Penicillium crustosum was resistant to all tested antibiotics.

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“…Extracellular solute-binding protein (number 3) was detected only in the shocked sludge. This protein has the ability to improve microbial resistance (Yang et al, 2013). The presence of proteins for anti-toxicity and the improvement of microbial resistance in shocked sludge indicate that the stress effect due to DMF was significant in the initial shocking stage.…”

Section: Ms Analysis and Protein Identificationmentioning

confidence: 98%

Contrasting sludge toxicity under various starting modes (shocking or acclimating) and original organics (with or without N, N-dimethylformamide (DMF))

Chen

Zhao

et al. 2015

International Biodeterioration & Biodegradation

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Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip Sites

Cited by 12 publications

References 6 publications

Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions

Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions

Isolation and Identification of Heavy Metals and Antibiotics Resistant Strains from Antananarivo Dumpsite, Madagascar

Contrasting sludge toxicity under various starting modes (shocking or acclimating) and original organics (with or without N, N-dimethylformamide (DMF))

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