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Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea.

Farasin J, Andres J, Casiot C, Barbe V, Faerber J, Halter D, Heintz D, Koechler S, Lièvremont D, Lugan R, Marchal M, Plewniak F, Seby F, Bertin PN, Arsène-Ploetze F - Front Microbiol (2015)

Bottom Line: The urease activity of Thiomonas sp.In AMD water supplemented with urea, the degradation of urea promotes iron, aluminum and arsenic precipitation.Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Université de Strasbourg - Centre National de la Recherche Scientifique, Institut de Botanique Strasbourg, France.

ABSTRACT
The acid mine drainage (AMD) in Carnoulès (France) is characterized by the presence of toxic metals such as arsenic. Several bacterial strains belonging to the Thiomonas genus, which were isolated from this AMD, are able to withstand these conditions. Their genomes carry several genomic islands (GEIs), which are known to be potentially advantageous in some particular ecological niches. This study focused on the role of the "urea island" present in the Thiomonas CB2 strain, which carry the genes involved in urea degradation processes. First, genomic comparisons showed that the genome of Thiomonas sp. CB2, which is able to degrade urea, contains a urea genomic island which is incomplete in the genome of other strains showing no urease activity. The urease activity of Thiomonas sp. CB2 enabled this bacterium to maintain a neutral pH in cell cultures in vitro and prevented the occurrence of cell death during the growth of the bacterium in a chemically defined medium. In AMD water supplemented with urea, the degradation of urea promotes iron, aluminum and arsenic precipitation. Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.

No MeSH data available.


Related in: MedlinePlus

Genes involved in urea degradation in CB2 and urea degradation activity in Thiomonas strains. (A) Genes involved in urea import (urt) and degradation (ure, in blue or genes encoding the urea amidolyase involved in the UCA-allophanate hydrolase pathway, in green) were detected in a genomic island in the CB2 genome. (B) After growth of cell cultures in m126 supplemented with urea (1 g.L−1), urea degradation activity was detected using Bromo-cresol purple as described in Materials and Methods. The purple color indicates urea degradation. In the negative control where no urea was added to the BCP reagent, the orange color stands for no activity observed (as indicated by “urease test—urea”). Urea degradation affected the pH of the media when cells were incubated in the synthetic medium m126 supplemented with urea. (C) Urea was detected in the the supernatant of CB2, 3As, or K12 cell cultures in synthetic medium m126 supplemented with 1 g.L−1 urea, at T0 and after 1, 2, or 3 days using mass spectrometry (UPLC-MS/MS). The data are expressed as the percentages of urea (area under the peak) measured at T0.
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Figure 1: Genes involved in urea degradation in CB2 and urea degradation activity in Thiomonas strains. (A) Genes involved in urea import (urt) and degradation (ure, in blue or genes encoding the urea amidolyase involved in the UCA-allophanate hydrolase pathway, in green) were detected in a genomic island in the CB2 genome. (B) After growth of cell cultures in m126 supplemented with urea (1 g.L−1), urea degradation activity was detected using Bromo-cresol purple as described in Materials and Methods. The purple color indicates urea degradation. In the negative control where no urea was added to the BCP reagent, the orange color stands for no activity observed (as indicated by “urease test—urea”). Urea degradation affected the pH of the media when cells were incubated in the synthetic medium m126 supplemented with urea. (C) Urea was detected in the the supernatant of CB2, 3As, or K12 cell cultures in synthetic medium m126 supplemented with 1 g.L−1 urea, at T0 and after 1, 2, or 3 days using mass spectrometry (UPLC-MS/MS). The data are expressed as the percentages of urea (area under the peak) measured at T0.

Mentions: The genomes of several closely related Thiomonas strains, seven originating from the same AMD (CB1, CB2, CB3, CB6, 3As, ACO3, ACO7) (Freel et al., in press) and one isolated from a sewage pipeline (Tm. intermedia K12), have been recently sequenced. A comparative analysis of these genomes using RGP finder (see Materials and Methods) showed the presence of 19 GEIs in the Tm. sp. CB2 genome (Freel et al., in press). One GEI 88.2 Kb in size (95 CDS) detected using this comparative genomic approach, which is present in the vicinity of another GEI (RGP10; Freel et al., in press) involved in arsenic resistance, was found to have the following characteristics: it is flanked by a miscRNA gene, contains several transposases and shows a compositional bias indicating possible acquisition by HGT (see Supplementary Table 1). Interestingly, this genomic island carries genes involved in urea degradation. In this study, we therefore refer to this GEI as the “urea island.” Two distinct enzymes, urease and urea amidolyase, are known to degrade urea into ammonia and carbonic acid. In bacteria, the urea amidolyase activity results from two separate enzymes, a urea carboxylase and an allophanate hydrolase (Kanamori et al., 2004). The “urea island” in Tm. sp. CB2 carries genes encoding these enzymes (ure genes encoding urease and two genes which are essential to the urea carboxylase (UCA)-allophanate hydrolase pathway) and urt genes involved in urea import (Figure 1A). A second copy of the urtABCDE genes was present at another locus in the CB2 genome (from 2246372 to 2251947). This duplication was not detected in the genomes of the other strains tested. The urea island also carries genes involved in metal, sulfur, lipid and nitrogen metabolism, including 27 genes involved in nitrate transport and reduction in particular. It also contains genes encoding ABC transporters and several hydrolases that contribute to the degradation of various compounds such as cyanate and creatinine (Supplementary Table 1).


Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea.

Farasin J, Andres J, Casiot C, Barbe V, Faerber J, Halter D, Heintz D, Koechler S, Lièvremont D, Lugan R, Marchal M, Plewniak F, Seby F, Bertin PN, Arsène-Ploetze F - Front Microbiol (2015)

Genes involved in urea degradation in CB2 and urea degradation activity in Thiomonas strains. (A) Genes involved in urea import (urt) and degradation (ure, in blue or genes encoding the urea amidolyase involved in the UCA-allophanate hydrolase pathway, in green) were detected in a genomic island in the CB2 genome. (B) After growth of cell cultures in m126 supplemented with urea (1 g.L−1), urea degradation activity was detected using Bromo-cresol purple as described in Materials and Methods. The purple color indicates urea degradation. In the negative control where no urea was added to the BCP reagent, the orange color stands for no activity observed (as indicated by “urease test—urea”). Urea degradation affected the pH of the media when cells were incubated in the synthetic medium m126 supplemented with urea. (C) Urea was detected in the the supernatant of CB2, 3As, or K12 cell cultures in synthetic medium m126 supplemented with 1 g.L−1 urea, at T0 and after 1, 2, or 3 days using mass spectrometry (UPLC-MS/MS). The data are expressed as the percentages of urea (area under the peak) measured at T0.
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Related In: Results  -  Collection

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Figure 1: Genes involved in urea degradation in CB2 and urea degradation activity in Thiomonas strains. (A) Genes involved in urea import (urt) and degradation (ure, in blue or genes encoding the urea amidolyase involved in the UCA-allophanate hydrolase pathway, in green) were detected in a genomic island in the CB2 genome. (B) After growth of cell cultures in m126 supplemented with urea (1 g.L−1), urea degradation activity was detected using Bromo-cresol purple as described in Materials and Methods. The purple color indicates urea degradation. In the negative control where no urea was added to the BCP reagent, the orange color stands for no activity observed (as indicated by “urease test—urea”). Urea degradation affected the pH of the media when cells were incubated in the synthetic medium m126 supplemented with urea. (C) Urea was detected in the the supernatant of CB2, 3As, or K12 cell cultures in synthetic medium m126 supplemented with 1 g.L−1 urea, at T0 and after 1, 2, or 3 days using mass spectrometry (UPLC-MS/MS). The data are expressed as the percentages of urea (area under the peak) measured at T0.
Mentions: The genomes of several closely related Thiomonas strains, seven originating from the same AMD (CB1, CB2, CB3, CB6, 3As, ACO3, ACO7) (Freel et al., in press) and one isolated from a sewage pipeline (Tm. intermedia K12), have been recently sequenced. A comparative analysis of these genomes using RGP finder (see Materials and Methods) showed the presence of 19 GEIs in the Tm. sp. CB2 genome (Freel et al., in press). One GEI 88.2 Kb in size (95 CDS) detected using this comparative genomic approach, which is present in the vicinity of another GEI (RGP10; Freel et al., in press) involved in arsenic resistance, was found to have the following characteristics: it is flanked by a miscRNA gene, contains several transposases and shows a compositional bias indicating possible acquisition by HGT (see Supplementary Table 1). Interestingly, this genomic island carries genes involved in urea degradation. In this study, we therefore refer to this GEI as the “urea island.” Two distinct enzymes, urease and urea amidolyase, are known to degrade urea into ammonia and carbonic acid. In bacteria, the urea amidolyase activity results from two separate enzymes, a urea carboxylase and an allophanate hydrolase (Kanamori et al., 2004). The “urea island” in Tm. sp. CB2 carries genes encoding these enzymes (ure genes encoding urease and two genes which are essential to the urea carboxylase (UCA)-allophanate hydrolase pathway) and urt genes involved in urea import (Figure 1A). A second copy of the urtABCDE genes was present at another locus in the CB2 genome (from 2246372 to 2251947). This duplication was not detected in the genomes of the other strains tested. The urea island also carries genes involved in metal, sulfur, lipid and nitrogen metabolism, including 27 genes involved in nitrate transport and reduction in particular. It also contains genes encoding ABC transporters and several hydrolases that contribute to the degradation of various compounds such as cyanate and creatinine (Supplementary Table 1).

Bottom Line: The urease activity of Thiomonas sp.In AMD water supplemented with urea, the degradation of urea promotes iron, aluminum and arsenic precipitation.Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Université de Strasbourg - Centre National de la Recherche Scientifique, Institut de Botanique Strasbourg, France.

ABSTRACT
The acid mine drainage (AMD) in Carnoulès (France) is characterized by the presence of toxic metals such as arsenic. Several bacterial strains belonging to the Thiomonas genus, which were isolated from this AMD, are able to withstand these conditions. Their genomes carry several genomic islands (GEIs), which are known to be potentially advantageous in some particular ecological niches. This study focused on the role of the "urea island" present in the Thiomonas CB2 strain, which carry the genes involved in urea degradation processes. First, genomic comparisons showed that the genome of Thiomonas sp. CB2, which is able to degrade urea, contains a urea genomic island which is incomplete in the genome of other strains showing no urease activity. The urease activity of Thiomonas sp. CB2 enabled this bacterium to maintain a neutral pH in cell cultures in vitro and prevented the occurrence of cell death during the growth of the bacterium in a chemically defined medium. In AMD water supplemented with urea, the degradation of urea promotes iron, aluminum and arsenic precipitation. Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.

No MeSH data available.


Related in: MedlinePlus