NV Space Grant Highlight: Genomic Characterization of Earths Deep Continental Subsurface Microbes

Overview:

My name is Alireza Saidi-Mehrabad and I’m a microbiologist and biotechnologist exploring some of the most extreme environments on Earth — terrestrial analogs for potential extraterrestrial habitats on, for example, Mars or the icy moons. Currently, I’m a postdoctoral researcher in Dr. Duane Moser’s lab at the Desert Research Institute (DRI), where I study microbes that live deep underground in fractured rock aquifers. These subsurface microbes live in complete darkness and survive using rock-hosted chemical reactions that might also occur on Mars, Europa, or Enceladus. By studying the genetic makeup of deep life on Earth, we can gain a better understanding of how life has evolved here, gain insights into the forms of life that might exist elsewhere in the Solar System, learn how to prevent contaminating other planets during exploration, and enhance our ability to recognize alien life if we ever encounter it.

Path to current research:

During my Master’s degree at the University of Calgary, I studied methane-consuming microbes that remove potent greenhouse gas from oil-contaminated water containing toxic chemicals like benzene and naphthalene. My research led to the discovery and characterization of Methylicorpusculum oleiharenae XLMV4, the first methane-consuming microbe ever identified in oil-contaminated water. For my PhD at the University of Alberta, I studied ancient microbes preserved in arctic permafrost dating back to the last ice age. These microbes had survived the dramatic climate shift that marked the end of the Ice Age and the start of the current warm period known as the Holocene. Using these ancient microbes as a model, I explored how today’s arctic soil microbes might respond to modern climate warming. I joined Dr. Moser’s lab to expand my knowledge of deep continental subsurface systems, one of the least studied ecosystems on Earth and likely on any other planetary body. Deep subsurface microbes, also known as deep life, differ from surface-dwelling microbes in that they persist under multiple harsh conditions, including high temperatures, extreme pH, high pressure, limited access to organic carbon, and—most importantly—disconnection from the Sun, which fuels life on Earth.

Mission Directorate:

My research aligns with the scope and responsibilities of the Planetary Science Division (PSD) within the Science Mission Directorate (SMD). Planetary Science is particularly responsible for missions and research investigating the potential for life in the solar system, Mars/icy moons mentioned previously. Deep life is of particular interest to NASA and the field of Astrobiology as it supports scientific research and mission development focused on understanding the origins of life in the solar system and maybe even beyond Earth. Successive Astrobiology Roadmaps have concluded that the most likely habitable zones in our solar system are where water exists — that is, in the subsurface of icy or rocky worlds. Astrobiology research uses the marine subsurface as an analog for icy worlds and the continental subsurface as an analog for rocky planets. Unfortunately, most deep continental subsurface microbes remain uncultured because we do not yet know how to grow and domesticate them in the laboratory. These microbes could serve as exceptional models for studying survival strategies relevant to planetary habitability, while also acting as a genomic archive of conditions resembling those of the primordial Earth. However, until they can be successfully cultivated, the full scope of their genomic potential, physiology, and cellular traits will remain inaccessible. To circumvent this problem, we must access their genomes directly without culturing, using technologies such as single-cell genomics or metagenomics. However, the question asked here, which method is better?

Findings/Results:

Two technologies were compared here: single-cell genomics combined with RedoxSensor Green (RSG), a new approach, and DNA-stable isotope probing (SIP) combined with metagenomics, a more established method. In both cases, RSG and SIP label microbes that are actively respiring and incorporating substrates — in our study, carbon monoxide, an important energy source in deep continental systems. My findings revealed a gap in current methodologies, highlighting limitations

in capturing the full diversity and metabolic potential of actively CO-utilizing microbes. Although Redox Sensor Green–based single-cell genomics (RSG-SCG) is rapid and avoids extensive laboratory manipulations, it failed to detect very rare active cells in samples treated with carbon monoxide. However, by combining SIP, 16S rRNA gene sequencing, and metagenomics, I was able to detect the rarest microbes that were initially undetectable in raw samples (representing less than 1% of the microbial community), including important groups such as methanogens, which are responsible for biological methane production and form a key part of the deep subsurface microbiome. Surprisingly, one of these rare bacteria, detected in SIP incubation bottles under a carbon monoxide atmosphere for about five months, BLM1B_11E, has close relatives that are only found in ultra-deep African mines. This enigmatic strain is also closely related to Candidatus Desulforudis DRI-14 (discovered at the Desert Research Institute by Dr. Hamilton-Brehm, whose genome I mapped for the first time) and Candidatus Desulforudis audaxviator (CDA).  This is important because CDA can fix carbon through the Wood-Ljungdahl pathway—the most ancient carbon fixation route used by the last universal common ancestor (~4 Ga)—reduce sulfate as a terminal electron acceptor (an ancient metabolic mechanism dating back 3.6–3.2 Ga), and fix nitrogen and CO using nitrogenase and CO dehydrogenases of archaeal origin, highlighting its evolutionary significance. This project taught me that no single method is perfect, but by combining proven traditional techniques with modern tools, we can gain a more complete picture of microbial life in extreme environments. The work not only improved the quality of the data we submitted to global DNA databases like the National Center for Biotechnology Information (NCBI) but also identified methods suitable for low biomass and unknown ecosystems. I am now preparing a scientific paper that describes the genome of Candidatus Desulforudis DRI-14 and its close relationship to CDA. Most importantly, have submitted the genome of DRI-14 to the NCBI database, where it can now support future research around the world. These preliminary data will support a larger Astrobiology proposal to NASA’s Solar System Science program focused on isolating and studying both DRI-14 and BLM1B_11E, two microbes that could change how we think about life in the deep subsurface and maybe even beyond Earth.

NASA Content and Resources Used:
This project was supported by the Nevada NASA Space Grant Consortium (Sponsor Award #80NSSC20M0043).