We may find deep-sea microbes resting in tombs they built themselves

Featured Image: Alvin – a submersible Human Occupancy Vehicle (HOV) designed to allow data collection at depths up to 6,500 m below the ocean surface. Featured image courtesy of John Magyar, Caltech.

Paper: Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Authors: Daniela Osorio-Rodriguez, Kyle S. Metcalfe, Shawn E. McGlynn, Hang Yu, Anne E. Dekas, Mark Ellisman, Tom Deerinck, Ludmilla Aristilde, John P. Grotzinger, and Victoria J. Orphan

Maybe one weekend in your life, you found yourself piling into an SUV at 6 AM with seven other students, intermittently registering the drone of an overenthusiastic geology professor whose course you took to fulfill a degree requirement. If so, in that vehicle, the proclamation that “the present is the key to the past” was certainly uttered. A recent study conducted by Daniela Osorio-Rodriguez and collaborators epitomizes the power of those words.

You likely have heard a great deal about carbon dioxide (CO2) and its effect on the climate as a greenhouse gas in the past few years. The second most commonly discussed greenhouse gas is methane (CH4), largely because it has ~28x the warming potential of CO2 over a 100-year timescale. For this reason, scientists have been interested in microorganisms that convert CH4 to CO2 as their means of obtaining energy to live – a process referred to as methane oxidation. These organisms play an important role in preventing the accumulation of methane in the atmosphere. In most soils, including the grass outside your home, methane oxidation occurs with the help of oxygen (aerobically). However, in sediments at the bottom of the ocean, oxygen is exhausted and methane-oxidizing bacteria must carry out this process anaerobically.

For over two decades, microbial ecologists have been studying the anaerobic oxidation of methane (AOM) by a syntrophic consortium of methanotrophic archaea and sulfate-reducing bacteria (ANME-SRB) living as aggregates around ocean floor methane seeps. The AOM leaves a chemical signature in the limestone rocks that the microbes live in. This signature has been used to identify ancient methane seeps throughout the geologic past. At these sites, geologists have searched for fossilized evidence of ANME-SRB aggregates in rocks. You can imagine this search being like looking for dinosaur bones, except the fossils you are looking for are microscopic.

For decades, geologists have collected rocks from ancient methane seeps all over the world and searched for ANME-SRB under the microscope. Despite significant effort, geologists have yet to observe fossilized aggregates of ANME-SRB. This is the mystery that Osorio-Rodriguez and collaborators are helping resolve in their recent paper. While they did not find fossils of ancient aggregates, they have found what we should be looking for! They observed microbially enhanced precipitation of silica (chemically similar to everyday glass) on the exterior of aggregates in lab cultures, carbonate rocks, and methane-rich sediments. By changing the water chemistry around them, the microbes cause silica to precipitate from the solution in the same way mineral coatings precipitate around a faucet if the water is ‘hard’. To determine the co-occurrence of ANME-SRB aggregates and silica, the authors interrogated laboratory cultures of ANME-SRB with a number of techniques.

  1. Fluorescence in situ hybridization (FISH) – This technique attaches a fluorescent molecule to a target DNA sequence, so that cells expressing this target DNA glow. Using target DNA for both ANME and SRB, the researchers can identify ANME-SRB aggregates as clusters of pink (ANME) and blue SRB) cells.
  2. Scanning Electron Microscopy (SEM) – This technique produces highly magnified images, allowing the researchers to identify ∼230 nanometer-sized amorphous silica spheres (small glass beads nearly 500x smaller than the thickness of a piece of paper) adjacent to the cell aggregates.
  3. Energy dispersive X-ray spectroscopy (EDS) – This technique allows scientists to make maps of elements (ex. silicon, carbon, etc.) around an aggregate while it is being photographed on the SEM.

Not only did the researchers observe the repeated precipitation of silica around the aggregates, by studying the chemistry of the artificial seawater, they could confirm that the silica could not be precipitating abiotically (without the presence of microbes) in their experiments. This allowed them to confirm that the cellular activity must play a role in the silica precipitation they observed. Also, they found that the silica precipitated near the aggregates is chemically different (containing less Mg, Al, and Fe) from other silicate minerals found at methane seeps.

Like all groundbreaking research, this study has raised new questions that have yet to be answered. While the authors are confident that the microbial activity is inducing the silica precipitation, how the microbes are doing this is still unknown. The eventual explanation will involve homing in on biochemical processes occurring in either ANME clusters, SRB clusters, or at the interface between the two that locally changed the water chemistry such that silica preservation is favorable. All that means is there is more exciting science be carried out.

Importantly, this research on modern aggregates has armed geologists with a new target in the search to identify fossilized consortia in the geologic past.

We may find deep-sea microbes resting in tombs they built themselves © 2024 by Joshua Anadu is licensed under CC BY-SA 4.0 

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