Scientists have identified new enzymes from deep-sea microbes that play a critical role in breaking down ethane, providing surprising insights into these organisms’ metabolism.
The deep sea floor features natural seeps that release alkanes, which are harmful pollutants with potential risks for life and contribute to global warming. Thankfully, the sediments surrounding these seeps are home to microbes that act as a natural filter: they consume the majority of these alkanes before they can enter the ocean and atmosphere. This process, known as anaerobic oxidation of alkanes, is significant, though poorly understood. Researchers from the Max Planck Institute for Marine Microbiology in Bremen, Germany, have now published a study detailing the breakdown of ethane, the second most prevalent alkane in these seeps. They investigated the enzymes involved in this process and discovered that their findings challenge long-held beliefs in anaerobic biochemistry. Their findings are shared in Nature Communications.
A missing piece in the energy-retrieving machinery suspected from genomic data
The anaerobic breakdown of ethane was first identified a few years ago, but many details remain unclear. “When we mapped out the chemical reactions in this pathway, we observed significant gaps in our understanding of the biochemistry involved. This led us to believe that these organisms must be obtaining energy through an unknown mechanism,” explains lead author Olivier Lemaire. The last two enzymes in the process produce carbon dioxide (CO2) from ethane. Other microbes utilize a protein called ferredoxin to capture electrons generated during the process. “This was also thought to hold true for ethane oxidizers. However, upon examining the genomes of these microbes, we found they lacked the necessary enzymes to harness energy using ferredoxin. Therefore, a different mechanism must be in play.”
A challenging study achieved through a successful scientific collaboration
Resolving this mystery required steadfast collaboration within the Max Planck Institute for Marine Microbiology. Gunter Wegener and his team collected the ethane-degrading microbial community from the deep sea and successfully cultured it in the lab, a task that proved to be quite challenging. Using these cultures, Tristan Wagner’s group was able to isolate and study the enzymes involved in ethane oxidation. “Extracting enzymes from such complex and precious microbial cultures is quite difficult, but we achieved it through significant effort and precision,” says Tristan Wagner.
A different enzymatic composition leads to a metabolic rewiring
The recent analyses reveal that both enzymes contain an additional protein, which is linked to the main enzyme through a metal wire composed of iron and sulfur. This subunit enables the use of an alternate electron acceptor: F420, a flavin-based molecule also significant for humans (like vitamin B2).
“The combination of CO2-producing enzymes with F420-reductases was previously unknown or unconsidered,” states Tristan Wagner. Further experiments confirmed that both enzymes utilize F420 as an electron acceptor. “This finding challenges established beliefs in anaerobic metabolism, as it broadens the potential functions of these enzymes.”
“We believe that coupling CO2 production with F420 as an electron acceptor may enhance the entire process. The electrons are then transferred across the cell membrane to another microbe for sulfate reduction, which is a common feature among alkane-oxidizing communities,” explains Gunter Wegener.
A milestone in the understanding of ethane degradation
By unraveling this metabolic enigma, Lemaire and his colleagues shine light on a crucial aspect of ethane-degrading microbes, which play a vital role in the carbon cycle. It also demonstrates that insights gained from a few model organisms cannot be directly applied to related species, as the enzymes involved can exhibit greater versatility than previously thought. “Our research highlights our limited understanding of these microbes’ metabolism, which have existed on Earth for billions of years and can adapt to various environments. It is essential to study them through experimental methods,” concludes Wagner.
This research holds significant implications, as the alkane oxidation performed by these microorganisms is a key component of the biological filter in marine seeps, helping to prevent large releases of naturally occurring alkanes into the atmosphere and ocean.
