Abstract
Over half of the organic carbon on Earth’s surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.
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The datasets generated during the current study are available in the GenBank repository, for which accession numbers are provided in Methods, Supplementary Table 1, and Supplementary Table 2.
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Acknowledgements
We thank Petróleo Brasileiro S.A. (PETROBRAS) for collecting the samples and financial support, and the colleagues at the Institute of Petroleum and Natural Resources (IPR-PUCRS) and the Immunology and Microbiology Laboratory for support and fruitful discussions. Particularly, we thank the IPR Geochemical Analysis Lab for technical assistance with methane cultures and the numerous contributors who helped preparing fieldwork materials. We also thank the Plant Biotechnology Lab (PUCRS) for the technical assistance with the siderophore production experiments.
Funding
This work was supported by PETROBRAS through the Conegás Project, the Institute of Petroleum and Natural Resources research fund, and the Academic Excellence Program by the Pontifical Catholic University of Rio Grande do Sul. AMP was supported by the Program for Institutional Internationalization (PrInt) Postdoctoral Fellowship provided by the CAPES Foundation, Ministry of Education, Brazil. Funding was also provided by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil, for PFRN and MMO master´s scholarships (CAPES-Finance Code 001).
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All authors contributed to the study conceptualization and design. Preparation of materials and experimental procedures were performed by AMP, MMO, PFRN, AG, RRO, CTO and LM. HMCBN, JMMK, and RMS acquired funding and provided resources and supervision. AMP and RMS drafted the manuscript, which was revised and approved by all authors.
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Author HMCBN is employed by the company PETROBRAS. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Proenca, A.M., Oliveira, M.M., Neves, P.F.R. et al. Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates. Arch Microbiol 204, 205 (2022). https://doi.org/10.1007/s00203-022-02814-z
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DOI: https://doi.org/10.1007/s00203-022-02814-z