Computational Systems Biology Lab

Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea–archaea and archaea–bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O₂, CO₂, and H₂S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiome.

Original Paper: 

• D. K. Kuppa Baskaran, S. Umale, Z. Zhou, K. Raman, and K. Anantharaman, “Metagenome-Based Metabolic Modelling Predicts Unique Microbial Interactions in Deep-Sea Hydrothermal Plume Microbiomes,” ISME Communications, vol. 3, iss. 1, pp. 1-14, 2023.
  [bibtex]

  @article{KuppaBaskaran2023Metagenomebased,
    title = {Metagenome-Based Metabolic Modelling Predicts Unique Microbial Interactions in Deep-Sea Hydrothermal Plume Microbiomes},
    author = {Kuppa Baskaran, Dinesh Kumar and Umale, Shreyansh and Zhou, Zhichao and Raman, Karthik and Anantharaman, Karthik},
    year = {2023},
    month = apr,
    journal = {ISME Communications},
    volume = {3},
    number = {1},
    pages = {1--14},
    publisher = {{Nature Publishing Group}},
    issn = {2730-6151},
    doi = {10.1038/s43705-023-00242-8},
    urldate = {2023-04-29},
    abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea\textendash archaea and archaea\textendash bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.},
    copyright = {2023 The Author(s)},
    langid = {english},
    keywords = {Metagenomics,Microbial ecology},
  }