Publicação
Genome-scale metabolic modelling of an extremophile microbial community
| Resumo: | Biomining offers an ecological alternative to the standard mining practices by using ex tremophiles that can endure elevated temperatures and low pH values. Several studies have been performed using Acidithiobacillus caldus SM-1 and Acidimicrobium ferrooxidans DSM 10331, suggesting that these bacteria in a community offer several advantages in bioleaching environ ments. Genome-Scale Metabolic (GSM) models simulate the organisms’ metabolism through constraint based approaches. Therefore, the reconstruction of GSM models for A. caldus and A. ferroox idans and their integration into a community will offer, besides valuable insights into their metabolism, a unique perspective on the potential interaction mechanisms between the two organisms within the community. In this work, we developed manually curated GSM models for A. caldus with 416 genes, 846 reactions and 646 metabolites, and A. ferrooxidans with 408 genes, 817 reactions and 640 metabolites. Both models were reconstructed using the user-friendly software merlin. We performed the functional annotation of both organisms’ genomes to identify their metabolic characteristics, which allowed generating a draft of the metabolic network. Manual curation efforts through literature, genomic information, phylogenetically close organisms and biological databases allowed refining the metabolic network. Furthermore, the models were validated using Cobrapy and Mewpy which allowed analysing flux distribution and interactions in different environmental conditions, and the results were compared with the literature and experimental data. Lastly, the community model was built using the organisms’ validated GSM models. In silico phenotypic simulations of the community model revealed that A. caldus exchanged lipid-production related compounds whilst A. ferrooxidans donated hydrogen sulfide assisting the former with its more complex sulfur metabolism. Moreover, the results suggest a more significant influence of A. ferrooxidans in the community’s growth rate whilst A. caldus assists A. ferrooxidans in biomass production. These models can serve as a starting point to study and model the community’s behaviour in several bioleaching conditions. |
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| Autores principais: | Nunes, Rui Ricardo Barros |
| Assunto: | Acidithiobacillus caldus SM-1 Acidimicrobium ferrooxidans DSM 10331 Extremophiles Genome-scale metabolic model Microbial community Biomining |
| Ano: | 2022 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | Biomining offers an ecological alternative to the standard mining practices by using ex tremophiles that can endure elevated temperatures and low pH values. Several studies have been performed using Acidithiobacillus caldus SM-1 and Acidimicrobium ferrooxidans DSM 10331, suggesting that these bacteria in a community offer several advantages in bioleaching environ ments. Genome-Scale Metabolic (GSM) models simulate the organisms’ metabolism through constraint based approaches. Therefore, the reconstruction of GSM models for A. caldus and A. ferroox idans and their integration into a community will offer, besides valuable insights into their metabolism, a unique perspective on the potential interaction mechanisms between the two organisms within the community. In this work, we developed manually curated GSM models for A. caldus with 416 genes, 846 reactions and 646 metabolites, and A. ferrooxidans with 408 genes, 817 reactions and 640 metabolites. Both models were reconstructed using the user-friendly software merlin. We performed the functional annotation of both organisms’ genomes to identify their metabolic characteristics, which allowed generating a draft of the metabolic network. Manual curation efforts through literature, genomic information, phylogenetically close organisms and biological databases allowed refining the metabolic network. Furthermore, the models were validated using Cobrapy and Mewpy which allowed analysing flux distribution and interactions in different environmental conditions, and the results were compared with the literature and experimental data. Lastly, the community model was built using the organisms’ validated GSM models. In silico phenotypic simulations of the community model revealed that A. caldus exchanged lipid-production related compounds whilst A. ferrooxidans donated hydrogen sulfide assisting the former with its more complex sulfur metabolism. Moreover, the results suggest a more significant influence of A. ferrooxidans in the community’s growth rate whilst A. caldus assists A. ferrooxidans in biomass production. These models can serve as a starting point to study and model the community’s behaviour in several bioleaching conditions. |
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