Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

Biology Direct

Didier Lièvremont¹  Marie-Claire Lett¹  François Delavat¹ 

[1]UMR7156 Université de Strasbourg/CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France

关键词: Bacterial diversity;    Actinobacteria;    Culture-dependent approaches;    Molecular biases;    Uncultured bacteria;    Rare biosphere;    Functional redundancy;    Neutrophilic bacteria;    Alkaliphilic bacteria;    Acid mine drainage (AMD);   

Others  :  796920
DOI  :  10.1186/1745-6150-7-28

 received in 2012-04-24, accepted in 2012-07-17,  发布年份 2012

【 摘 要 】

Background

Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions As(III) oxidation, cellulose degradation and cobalamine biosynthesis.

Results

Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness.

Conclusions

This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria may be part of the rare biosphere which remained previously undetected due to molecular biases. No matter their current ecological relevance, the exploration of the full diversity remains crucial to decipher the function and dynamic of any community. This work also underlines the importance to associate culture-dependent and -independent approaches to gain an integrative view of the community function.

Reviewers

This paper was reviewed by Sándor Pongor, Eugene V. Koonin and Brett Baker (nominated by Purificacion Lopez-Garcia).

【 授权许可】

   
2012 Delavat et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1 .

Figure 2 .

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