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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

In situ expression of the Thiomonas arsenite oxidase and urease-encoding genes. Agarose gel analysis of transcripts corresponding to aioA, ureC, and the gene encoding the allophanate hydrolase amplified by performing RT-PCR on the RNA extracted from the bacterial community inhabiting the Carnoulès AMD. Lane M: GeneRuler™ 1kb DNA Ladder Plus (Fermentas). Lane 2, 4, and 6: negative controls (with each gene, the same reaction was performed but without any reverse transcriptase). Lane 1: RT-PCR product in the case of aioA (555 bp). Lane 3: RT-PCR product in that of ureC (570 bp). Lane 5: RT-PCR product in that of the allophanate hydrolase gene (515 bp). The amplification products were sequenced and the sequences predicted were obtained (i. e., those of aioA and ureC).
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Figure 11: In situ expression of the Thiomonas arsenite oxidase and urease-encoding genes. Agarose gel analysis of transcripts corresponding to aioA, ureC, and the gene encoding the allophanate hydrolase amplified by performing RT-PCR on the RNA extracted from the bacterial community inhabiting the Carnoulès AMD. Lane M: GeneRuler™ 1kb DNA Ladder Plus (Fermentas). Lane 2, 4, and 6: negative controls (with each gene, the same reaction was performed but without any reverse transcriptase). Lane 1: RT-PCR product in the case of aioA (555 bp). Lane 3: RT-PCR product in that of ureC (570 bp). Lane 5: RT-PCR product in that of the allophanate hydrolase gene (515 bp). The amplification products were sequenced and the sequences predicted were obtained (i. e., those of aioA and ureC).

Mentions: The present data suggest that the bacterial degradation of urea may accelerate iron, arsenic, and aluminum precipitation in AMD in the presence of urea. Since urea was detected in the interstitial water of sediments from the AMD-impacted creek, it may be available to bacteria inhabiting this AMD to use for degradation purposes (Halter et al., 2012). However, the effects of urea degradation on metal precipitation were observed in this study under laboratory conditions using a higher urea concentration than that previously measured in situ (Halter et al., 2012). In addition, some of the Thiomonas strains inhabiting AMD waters are able to degrade urea whereas others are not, which suggests that urea degradation activity is not crucial to the survival of Thiomonas in AMD environments. In order to determine whether these biological activities are relevant in situ, the levels of expression of the Thiomonas genes encoding the arsenite oxidase and urease were therefore examined by performing RT-PCR with RNA extracted from the Reigous creek sediment community, as previously (Bertin et al., 2011). These Thiomonas cells extracted from the Reigous creek sediment were found to express the two genes aioA and ureC (Figure 11) responsible for the two activities promoting toxic metal precipitation, i.e., arsenite oxidation and urea degradation, respectively. These findings suggest that some of the organisms in the Carnoulès AMD community are able to produce large enough amounts of urea to promote the expression of ure genes in situ. CB2 may benefit indirectly from microbial activities in microscale environmental niches where the urea concentrations may be higher than those previously measured in the macroscale environment. This bacterium is known to be able to form biofilms, for instance (Marchal et al., 2011): other organisms surrounding Thiomonas cells in biofilms may provide metabolites such as urea or make the environmental conditions more suitable for CB2 survival and growth. These organisms may in turn benefit from the urea degradation and arsenite oxidation activities performed by Thiomonas, since both activities accelerate the precipitation of toxic metals. The urea degradation process promoted by Thiomonas may therefore contribute to enhancing the survival or the fitness of other microorganisms in the surrounding biofilm community, as previously suggested to occur in the case of other activities and other multi-species biofilms exposed to toxic metals (Koechler et al., 2015). Previous studies have established that the protist E. mutabilis present in the Carnoulès AMD is a primary producer excreting organic compounds which may be consumed by bacterial species (Bertin et al., 2011; Halter et al., 2012). Among the organic substances produced by this protist, urea was found to be excreted in synthetic medium (Halter et al., 2012). Other bacteria belonging to this community, namely “Candidatus Fodinabacter communificans” (Carn1 and Carn4), also carry genes involved in urea production (Bertin et al., 2011). If one of these organisms produces urea, this compound may then be degraded by Thiomonas. Since several organisms may be responsible of urea production, some of which have not yet been grown and studied in vitro, a new experimental approach will be required to identify the source(s) of urea and the relevance of its degradation to the survival of Thiomonas in AMDs. Generally speaking, the results presented here confirm the complexity of these processes, which probably involve interactions both between Thiomonas and the urea producers (E. mutabilis or other less well documented bacteria such as “Candidatus Fodinabacter communificans”) and with other mechanisms (such as arsenite oxidation). In conclusion, it emerges that several closely related Thiomonas strains co-exist in the Carnoulès AMD waters, which have different abilities in this toxic environment. Recent studies have shown that several closely-related bacteria co-existing in AMD biofilms express different proteins and therefore play distinct ecological roles (Denef et al., 2010). Further studies on this fine-scale heterogeneity and the interactions occurring between Thiomonas strains and other members of the AMD community will now be required in order to understand more clearly how these communities function and survive in these highly toxic ecosystems.


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)

In situ expression of the Thiomonas arsenite oxidase and urease-encoding genes. Agarose gel analysis of transcripts corresponding to aioA, ureC, and the gene encoding the allophanate hydrolase amplified by performing RT-PCR on the RNA extracted from the bacterial community inhabiting the Carnoulès AMD. Lane M: GeneRuler™ 1kb DNA Ladder Plus (Fermentas). Lane 2, 4, and 6: negative controls (with each gene, the same reaction was performed but without any reverse transcriptase). Lane 1: RT-PCR product in the case of aioA (555 bp). Lane 3: RT-PCR product in that of ureC (570 bp). Lane 5: RT-PCR product in that of the allophanate hydrolase gene (515 bp). The amplification products were sequenced and the sequences predicted were obtained (i. e., those of aioA and ureC).
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Figure 11: In situ expression of the Thiomonas arsenite oxidase and urease-encoding genes. Agarose gel analysis of transcripts corresponding to aioA, ureC, and the gene encoding the allophanate hydrolase amplified by performing RT-PCR on the RNA extracted from the bacterial community inhabiting the Carnoulès AMD. Lane M: GeneRuler™ 1kb DNA Ladder Plus (Fermentas). Lane 2, 4, and 6: negative controls (with each gene, the same reaction was performed but without any reverse transcriptase). Lane 1: RT-PCR product in the case of aioA (555 bp). Lane 3: RT-PCR product in that of ureC (570 bp). Lane 5: RT-PCR product in that of the allophanate hydrolase gene (515 bp). The amplification products were sequenced and the sequences predicted were obtained (i. e., those of aioA and ureC).
Mentions: The present data suggest that the bacterial degradation of urea may accelerate iron, arsenic, and aluminum precipitation in AMD in the presence of urea. Since urea was detected in the interstitial water of sediments from the AMD-impacted creek, it may be available to bacteria inhabiting this AMD to use for degradation purposes (Halter et al., 2012). However, the effects of urea degradation on metal precipitation were observed in this study under laboratory conditions using a higher urea concentration than that previously measured in situ (Halter et al., 2012). In addition, some of the Thiomonas strains inhabiting AMD waters are able to degrade urea whereas others are not, which suggests that urea degradation activity is not crucial to the survival of Thiomonas in AMD environments. In order to determine whether these biological activities are relevant in situ, the levels of expression of the Thiomonas genes encoding the arsenite oxidase and urease were therefore examined by performing RT-PCR with RNA extracted from the Reigous creek sediment community, as previously (Bertin et al., 2011). These Thiomonas cells extracted from the Reigous creek sediment were found to express the two genes aioA and ureC (Figure 11) responsible for the two activities promoting toxic metal precipitation, i.e., arsenite oxidation and urea degradation, respectively. These findings suggest that some of the organisms in the Carnoulès AMD community are able to produce large enough amounts of urea to promote the expression of ure genes in situ. CB2 may benefit indirectly from microbial activities in microscale environmental niches where the urea concentrations may be higher than those previously measured in the macroscale environment. This bacterium is known to be able to form biofilms, for instance (Marchal et al., 2011): other organisms surrounding Thiomonas cells in biofilms may provide metabolites such as urea or make the environmental conditions more suitable for CB2 survival and growth. These organisms may in turn benefit from the urea degradation and arsenite oxidation activities performed by Thiomonas, since both activities accelerate the precipitation of toxic metals. The urea degradation process promoted by Thiomonas may therefore contribute to enhancing the survival or the fitness of other microorganisms in the surrounding biofilm community, as previously suggested to occur in the case of other activities and other multi-species biofilms exposed to toxic metals (Koechler et al., 2015). Previous studies have established that the protist E. mutabilis present in the Carnoulès AMD is a primary producer excreting organic compounds which may be consumed by bacterial species (Bertin et al., 2011; Halter et al., 2012). Among the organic substances produced by this protist, urea was found to be excreted in synthetic medium (Halter et al., 2012). Other bacteria belonging to this community, namely “Candidatus Fodinabacter communificans” (Carn1 and Carn4), also carry genes involved in urea production (Bertin et al., 2011). If one of these organisms produces urea, this compound may then be degraded by Thiomonas. Since several organisms may be responsible of urea production, some of which have not yet been grown and studied in vitro, a new experimental approach will be required to identify the source(s) of urea and the relevance of its degradation to the survival of Thiomonas in AMDs. Generally speaking, the results presented here confirm the complexity of these processes, which probably involve interactions both between Thiomonas and the urea producers (E. mutabilis or other less well documented bacteria such as “Candidatus Fodinabacter communificans”) and with other mechanisms (such as arsenite oxidation). In conclusion, it emerges that several closely related Thiomonas strains co-exist in the Carnoulès AMD waters, which have different abilities in this toxic environment. Recent studies have shown that several closely-related bacteria co-existing in AMD biofilms express different proteins and therefore play distinct ecological roles (Denef et al., 2010). Further studies on this fine-scale heterogeneity and the interactions occurring between Thiomonas strains and other members of the AMD community will now be required in order to understand more clearly how these communities function and survive in these highly toxic ecosystems.

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