Adaptation in toxic environments: Arsenic genomic islands in the bacterial genus Thiomonas:

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

Spatio-Temporal Detection of the Thiomonas Population and the Thiomonas Arsenite Oxidase Involved in Natural Arsenite Attenuation Processes in the Carnoulès Acid Mine Drainage

International audienceThe acid mine drainage (AMD) impacted creek of the Carnoulès mine (Southern France) is characterized by acid waters with a high heavy metal content. The microbial community inhabiting this AMD was extensively studied using isolation, metagenomic and metaproteomic methods, and the results showed that a natural arsenic (and iron) attenuation process involving the arsenite oxidase activity of several Thiomonas strains occurs at this site. A sensitive quantitative Selected Reaction Monitoring (SRM)-based proteomic approach was developed for detecting and quantifying the two subunits of the arsenite oxidase and RpoA of two different Thiomonas groups. Using this approach combined with 16S rRNA gene sequence analysis based on pyrosequencing and FISH, it was established here for the first time that these Thiomonas strains are ubiquitously present in minor proportions in this AMD and that they express the key enzymes involved in natural remediation processes at various locations and time points. In addition to these findings, this study also confirms that targeted proteomics applied at the community level can be used to detect weakly abundant proteins in situ

Schematic diagram of ICE19 in CB2.

<p>This figure shows one part of the arsenic island of CB2 (RGP19) that has the characteristics of an ICE (called ICE19) (A) Alignment of ICE19 of <i>Thiomonas</i> sp. CB2 with its cognate portion found in the strain 3As (ThGEI-O). The arsenic island RGP19 of CB2 is localized in a different genomic region that ThGEI-O in 3As. The ThGEI-O of 3As (upper portion of the figure) is localized in a gene encoding a 4Fe-4S ferredoxin which is intact in CB2. Direct repeat sequences are indicated. (B) Sequence comparison of the almost perfect direct repeat flanking the ICE19. <i>attL</i>: left DR; <i>attR</i>: right DR. (C) Schematic representation of the integrated and circular form of the ICE19 of CB2, which were detected by PCR. The sequence <i>attI</i> is identical to <i>attR</i> and <i>attB</i> identical to <i>attL</i>. The % of nucleotide identity is expressed along a grey scale. Figures were generated with Easyfig [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139011#pone.0139011.ref050" target="_blank">50</a>].</p

Percent of identity between AioA and AioB of CB2, 3As and K12.

<p>Whereas both 3As and K12 encoded a single copy of AioA and AioB, CB2 encoded two copies of each protein, one in RGP19 and another in RGP10. AioA and AioB of CB2 encoded in the RGP19 shared more identity with AioA and AioB of 3As (99.9% and 100% respectively). However, AioA and AioB encoded on the RGP10 share more identity with AioA and AioB of K12 (86.9% and 98.3% respectively).</p

Comparison among the CB2, K12, and 3As genomes.

<p>(A) Dot plot, CB2 vs 3As and 3As vs K12. The genomes of 3As and K12 are well conserved while the CB2 genome appears to have undergone chromosomal rearrangements. (B) Scheme demonstrating the key differences between the <i>Thiomonas</i> ancestor and CB2 genome. Above, “1”, “2” and “3” highlight a translocation of 0.1 Mb, an inversion of 1.8 Mb and a translocation and inversion of 0.13 Mb, respectively. </p

CB2 capacity to oxidize arsenite.

<p>Concentrations of As(III) (squares) and As(V) (triangles) are shown for CB2 cells grown in m126 medium in the presence of 2.66 mM of As(III) (full symbols) and m126 medium in the presence of 2.66 mM of As(III) and supplemented with glucose (hollow symbols). Error bars indicate standard deviations of triplicate cultures. No As(III) oxidation was observed in abiotic controls (data not shown).</p