The next 4 years of funding for our Methanomethylicia research are secured – more on that soon! We are always looking for enthusiastic grad students and postdocs to join our lab. Email me a CV & a 1-2 pages motivation/research letter (I will not answer DMs) http://www.environmental-microbiology.com
Hot spring metagenomics was done together with the JGI via a FICUS grant to me and a CSP to Viola, Anthony, Zackary Jay and myself. None of the bioinformatics in my lab would be possible without my awesome staff scientist Zackary Jay, who co-authors both studies.
My lab’s research on these new methanogens was sponsored by the NASA Exobiology program, with minor support from awards from the Simons Foundation and the Thermal Biology Institute at Montana State University.
several years ago from another hot spring. LCB3 is very closely related to MDKW but from a different hot spring and grows on methanol and hydrogen at 77C. LCB3 extends the upper temperature limit of both methyl-reducing and b-type cytochrome-involving methanogenesis.
To the best of our knowledge, this is the only culture of a korarchaeon (methanogenic or not) – the only other one, Korarchaeum cryptofilum, was lost many years ago. LCB3 is a close relative of another strain, MDKW, which is represented by a MAG obtained by Luke McKay
CULTURE 3. Ca. Methanodesulfokora washburnensis LCB3 falls within the Korarchaeia! The methanogen was cultured by my (previous) postdoc Viola Krukenberg. After she left the lab experiments were continued by Anthony Kohtz who shares 1st authorship. http://tinyurl.com/4v4fkda6
I want to give a big shoutout to Lei Cheng & Diana Sousa who, after learning we also had a culture of a novel methanogen within the Thermoproteota, did not rush to be the first to publish but offered to publish jointly. This is how science should be done. Thank you, Lei and Diana!
Although theirs and our archaeon fall within the same genus, they clearly have important ecophysiological differences: they grow at different temperatures and use different substrates, for example.
CULTURE 2. The labs of Lei Cheng and Diana Sousa, with co-first authors Kejia Wu and Lei Zhou, cultured another member of the Methanomethylicia, Ca. Methanosuratincola petrocarbonis from a Chinese oil reservoir. And it’s a pure culture! http://tinyurl.com/mtsrj6b9
and that they form cell-to-cell bridges. One of these bridges connected three cells and in the connection between the three cells we found ribosomes and unknown filaments, which we believe (but yet haven’t proven) are proteinaceous.
Collaborator Martin Pilhofer and his grad student Nick Petrosian (not on twitter) obtained beautiful cryo-electron tomography images that show that cells have virus-like particles in and on them, have archaealla and chemotaxis arrays
is a bona fide methanogen. Using growth experiments, stable isotope tracing (GCMS), genomic annotation, transcriptomics, bioorthogonal labeling, fluorescence in situ hybridization, etc. we should that it is using methanol and hydrogen to perform methyl-reducing methanogenesis.
CULTURE 1. Ca. Methanosuratincola verstraetei was cultured by Anthony Kohtz from a Yellowstone hot spring. It’s co-enriched with a Euryarchaeotal methanogen, Methanothermobacter, and we spent a lot of work convincing ourselves that Methanosuratincola http://tinyurl.com/yr4p7js6
as well a model for Early Earth, where these metabolisms first evolved. For my lab, we work under research permit YELL-SCI-8010 in Yellowstone National Park. Now that this is out of the way, let’s talk about the three cultures.
As reminder, high temperature ecosystems like hot springs are excellent microbial study systems because of their comparatively low taxonomic diversity (10s to 1000s of species only). They are also excellent model systems as astrobiology analog sites (e.g. for Europa’s deep ocean)
suggests that Methanomethylicia are widely distributed in anoxic environments, where they might (experimentally untested) contribute to methane cyling. Korarchaeia, in turn, are restricted to high temperature ecosystems like terrestrial hot springs and marine hot vents.
we cultured two methanogens from within the Methanomethylicia (previously Verstraetearchaeota; one by Lei, one by us) within the Thermoproteota/TACK superphylum and one by us from within the Korchaeia (also within the Thermoproteota).All 3 are thermophiles but indirect evidence -FIG by Anthony Kohtz
which we only know from their DNA, are actually methanogens. The labs of Lei Cheng (not on Twitter) & @SousaDZand, working independently but publishing jointly, my lab changed that now. Using biomass from two hot springs and an oil reservoir, and after years of hard work,
or anaerobic respiration. That’ in stark contrast to virtually all known Euryarchaeotal methanogens who can ONLY live by fermentation. Thus, we need to be agnostic and test these genomic hypotheses about methanogenic potential to assess whether or not any of these new microbes,
according to their genome, can live by means other than methanogenesis. So see, you cannot have it both ways. If you comfy relying on genomics to predict metabolism, that’s fine. BUT, all of these lineages can do other things, like grow by fermentation or sulfite-reduction,
However, no experimental evidence was available to support this claim. Why is that a problem? Well, first we cannot rely on genomics and metabolic prediction to accurately predict function. And second, and that’s a big one in this case, all of these new lineages,
Missing above: In the past decade metagenomics revealed the genetic potential for methanogenesis in several phyla level lineages outside the Euryarchaeota, including members of the Bathyarchaeota, Verstraetearchaeota/Methanomethylicia, Korarchaeota, Helarchaeota (in Asgard), & Nezhaarchaeota.
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