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Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F - PLoS ONE (2015)

Bottom Line: CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes.We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7).Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France.

ABSTRACT
Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

No MeSH data available.


Maximum likelihood tree of the Thiomonas strains included in this study.The tree is based on the concatenated alignment of rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA genes (8628 nucleotide positions). The sequences were aligned with the MUSCLE and trimmed with GBLOCKS programs implemented in SEAVIEW software version 4.5.4 [46] and then concatenated. The tree was inferred with PhyML version 3.1 [47], using the GTR+Γ4 model as suggested by the proposed model tool implemented in TREEFINDER v2011 [48], using the NNI+SPR option for topology search. Values at branch nodes correspond to bootstrap values (100 replicates) calculated with PhyML and to posterior probabilities calculated with MrBayes version 3.2.2 [49], with the GTR + G4 model. The scale bar represents the average number of substitutions per site.
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pone.0139011.g001: Maximum likelihood tree of the Thiomonas strains included in this study.The tree is based on the concatenated alignment of rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA genes (8628 nucleotide positions). The sequences were aligned with the MUSCLE and trimmed with GBLOCKS programs implemented in SEAVIEW software version 4.5.4 [46] and then concatenated. The tree was inferred with PhyML version 3.1 [47], using the GTR+Γ4 model as suggested by the proposed model tool implemented in TREEFINDER v2011 [48], using the NNI+SPR option for topology search. Values at branch nodes correspond to bootstrap values (100 replicates) calculated with PhyML and to posterior probabilities calculated with MrBayes version 3.2.2 [49], with the GTR + G4 model. The scale bar represents the average number of substitutions per site.

Mentions: There were several strains used in this study that were previously isolated from the Carnoulès AMD: 3As, CB1, CB2, CB3, and CB6. Here, we also report two novel strains isolated from this AMD community: ACO3 and ACO7. Since the phylogeny of closely related strains is difficult to resolve using only the 16S rRNA gene, we combined five markers (rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA) to clarify the relationships among these Thiomonas strains (Fig 1). The resulting maximum likelihood and Bayesian trees showed that 3As, CB1, CB6, ACO3, and ACO7 are very closely related (bootstrap value (BV) = 99% and posterior probability (PP) = 1.0), and cluster with CB3 and CB2, while K12 is more divergent (BV = 82% and PP = 1.0).


Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F - PLoS ONE (2015)

Maximum likelihood tree of the Thiomonas strains included in this study.The tree is based on the concatenated alignment of rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA genes (8628 nucleotide positions). The sequences were aligned with the MUSCLE and trimmed with GBLOCKS programs implemented in SEAVIEW software version 4.5.4 [46] and then concatenated. The tree was inferred with PhyML version 3.1 [47], using the GTR+Γ4 model as suggested by the proposed model tool implemented in TREEFINDER v2011 [48], using the NNI+SPR option for topology search. Values at branch nodes correspond to bootstrap values (100 replicates) calculated with PhyML and to posterior probabilities calculated with MrBayes version 3.2.2 [49], with the GTR + G4 model. The scale bar represents the average number of substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589449&req=5

pone.0139011.g001: Maximum likelihood tree of the Thiomonas strains included in this study.The tree is based on the concatenated alignment of rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA genes (8628 nucleotide positions). The sequences were aligned with the MUSCLE and trimmed with GBLOCKS programs implemented in SEAVIEW software version 4.5.4 [46] and then concatenated. The tree was inferred with PhyML version 3.1 [47], using the GTR+Γ4 model as suggested by the proposed model tool implemented in TREEFINDER v2011 [48], using the NNI+SPR option for topology search. Values at branch nodes correspond to bootstrap values (100 replicates) calculated with PhyML and to posterior probabilities calculated with MrBayes version 3.2.2 [49], with the GTR + G4 model. The scale bar represents the average number of substitutions per site.
Mentions: There were several strains used in this study that were previously isolated from the Carnoulès AMD: 3As, CB1, CB2, CB3, and CB6. Here, we also report two novel strains isolated from this AMD community: ACO3 and ACO7. Since the phylogeny of closely related strains is difficult to resolve using only the 16S rRNA gene, we combined five markers (rpoA, dnaK, atpD, 16S rDNA, and 23S rDNA) to clarify the relationships among these Thiomonas strains (Fig 1). The resulting maximum likelihood and Bayesian trees showed that 3As, CB1, CB6, ACO3, and ACO7 are very closely related (bootstrap value (BV) = 99% and posterior probability (PP) = 1.0), and cluster with CB3 and CB2, while K12 is more divergent (BV = 82% and PP = 1.0).

Bottom Line: CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes.We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7).Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France.

ABSTRACT
Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

No MeSH data available.