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Unlocking the secrets of Earth's underground ecosystems
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Unlocking the secrets of Earth's underground ecosystems
by Clarence Oxford
Los Angeles CA (SPX) Apr 03, 2024

Scientists at the Bigelow Laboratory for Ocean Sciences have introduced a pioneering method to simultaneously measure and connect the genetics and functionality of microbes thriving in Earth's oxygen-deprived subsurface layers. This development, crucial for comprehending microbes' roles in significant global cycles like carbon processing, marks a significant advancement in microbiology.

The method, conceptualized at the Single Cell Genomics Center of Bigelow Laboratory, revealed that a sulfate-reducing bacterium species was the predominant and most active life form in a groundwater aquifer under Death Valley, situated nearly half a mile underground. Published in the Proceedings of the National Academy of Sciences, the research illustrates the method's potential in gauging organismal activity in harsh environments.

Melody Lindsay, a Research Scientist and the study's lead author, highlighted the novelty of the approach, explaining it allows for the differentiation of activity levels among microbial community members, thereby enhancing understanding of their potential impact on global biogeochemical cycles.

This inquiry is part of a broader initiative titled "Genomes to Phenomes," funded by NSF's EPSCoR program and in collaboration with the Desert Research Institute and the University of New Hampshire. It combines recent advances in single-cell genetic sequencing with inventive application of flow cytometry to estimate cellular processes such as respiration rates.

Adapting flow cytometry, originally from biomedical sciences, for environmental microbiology enabled the swift identification of living microbes in aquifer samples. These microbes were marked with a novel compound that reacts under laser light, indicating chemical reaction rates within. The fluorescence intensity correlation to reaction rates was established through experiments with lab-cultured cells, then applied to the Death Valley aquifer samples.

After isolating the active microbes, their genomes were sequenced, and meta-transcriptomics were employed to ascertain active gene expression. Radioisotope tracers were also used to validate the findings and provide deeper insights into microbial capabilities versus their actual activities.

The Single Cell Genomics Center stands as the unique facility globally offering this technique to the scientific community. Ramunas Stepanauskas, the center's director and project's principal investigator, expressed excitement over the study's contribution to demystifying vast underground microbial ecosystems.

This research builds upon previous work demonstrating the technique's efficacy in measuring the activity of individual cells in marine environments. The current study extends its application to environments with minimal biomass and anaerobic life forms. Preliminary findings had focused on oxygen-consuming marine microbes, with the current expansion to include organisms like the sulfate-reducing Candidatus Desulforudis audaxviator.

The team plans to further apply this methodology across various anaerobic processes and new settings, including Maine's coastal sediments. A NASA-funded project also explores its utility in studying the deep subsurface below oceans, with aspirations of extending its application to extraterrestrial environments.

Research Report:Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem

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