BacterioFiles 350 - Microbes Mysteriously Make Methane

Nitrogenase protein structure
By Jjsjjsjjs - Own work
CC BY-SA 3.0

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

Download Episode (11.8 MB, 12.9 minutes)

Show notes:
Microbe 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.

Other interesting stories:

• Gut bacterial metabolite helps protect mice against gut pathogen

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

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