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Sunday, 05 August 2018 21:41

Microbes Mysteriously Make Methane - BacterioFiles 350

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Published in Bacteriofiles

This episode: A version of the microbial enzyme that fixes nitrogen can also convert carbon dioxide to methane!

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(11.8 MB, 12.9 minutes)

Show notes: 

bf350nitrogenaseMicrobe of the episode: Human mastadenovirus D

Journal Paper:
Zheng Y, Harris DF, Yu Z, Fu Y, Poudel S, Ledbetter RN, Fixen KR, Yang Z-Y, Boyd ES, Lidstrom ME, Seefeldt LC, Harwood CS. 2018. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat Microbiol 3:281–286.

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Episode outline:

  • Background: Microbes do things nothing else does
    • consume methane – bacteria called methanotrophs
    • Create methane – archaea called methanogens living in anaerobic marshes and guts
      • Also some other minor pathways
    • Important cos more potent greenhouse gas than CO2, also fuel
  • Also fixing N2 gas – high-energy process, only microbes can do it
    • Makes ~half of nitrogen fixed in world; other half is industrial fertilizer :O
    • Nitrogenases are cool - ammonia, nitrogen source for protein etc from air
      • Core is cluster of metal atoms, mostly iron
      • But 3 different versions, each with unique central atom – Mo, V, and another Fe
      • Fixing species all have Mo, only some have V or Fe or both
        • No more than 9% of fixing species have Fe
      • All fix nitrogen, but have different protein sequences, structures, and kinetics
      • In lab, cells mostly use Mo whenever it's available, repress others (most efficient)
        • Others just backups?
      • But evidence of V more effective in cold, and both active unexpectedly
      • So consider possibility of other functions, more complex inter-relatedness in wild
  • What’s new: Now, scientists publishing in Nature Microbiology have discovered one interesting possible function of the iron-center nitrogenase: producing methane!
  • All versions actually not very specific to nitrogen
    • Test for any activity uses acetylene – 2 C with triple bond – conversion to ethylene
    • V and slightly Mo can reduce CO to ethylene + more
    • Other stuff too, depending on version
    • Mutated Mo can reduce CO2 to methane
  • Methods: Here, wanted to test if other versions can do same
  • Microbe is Rhodopseudomonas palustris – phototroph bacterium
  • Mutated V protein same as Mo version, 2 amino acids in active site
    • Wild V produced very small amounts of methane; mutant made a lot
  • Tried Fe protein too, same mutations
    • But mutant produced hardly any methane, while wild produced surprising amount
    • Apparently reduces CO2 naturally
  • But actually from CO2? Tested with stable isotope-labeled bicarbonate
    • Cells produced methane that showed up on MS as 1 neutron extra
  • Then purified nitrogenase and tested production
    • Produced a lot of ammonia and ~3x more hydrogen, and relatively little methane
    • But all three at once
  • Tested Fe nitrogenases from 3 other species too
    • Rhodospirillum rubrum, Rhodobacter capsulatus, and Azotobacter vinelandii
    • Each also showed methane production when growing with Fe nitrogenase
  • Finally tested co-culture with methanotroph
    • Methane produced by nitrogenase was enough to support growth
    • Confirmed using 13C-labeled methane
  • Summary: A version of the enzyme that converts nitrogen gas to biologically useful forms also converts CO2 to methane, a component of natural gas
  • Applications and implications: Not very efficient biofuel production by itself
    • But in addition to fertilizer and/or hydrogen production, maybe byproduct
  • What do I think: Raises interesting questions about history of nitrogenase
    • 1st weird that Mo version is oldest and most common
      • Harder to gather Fe + Mo vs. just Fe, seems like
    • But possible that alternates interact more than just N cycle
      • Link between C and N
      • Can produce methane that other organisms can consume
        • Symbiosis
      • Interesting interaction to study to see if it affects nitrogenase regulation
  • Microbes have some very interesting features
Last modified on Sunday, 05 August 2018 21:46
Jesse Noar

Jesse Noar is microbiologist with a PhD from North Carolina State University and Bachelor's from Cornell. Most of his research has focused on the amazing abilities and potential uses of bacteria, especially those found in soil. Jesse hosts the BacterioFiles podcast highlighting the most interesting recent microbiology research on all kinds of different microbes, part of the ASM family of podcasts. Learn more at or at