10:25:54 From Avi Flamholz to Everyone : just to clarify - the net reaction of metabolism may not be limited by energy, but it can be the case that individual metabolic reactions are near equilibrium even in the presence of O2
10:31:15 From Seppe Kuehn to Everyone : Are all arrows on this diagram required in a methanogenic community? Or are some communities assembled using a subset of these reactions to take polymer —> methane?
10:32:06 From Daan de Groot (phone, audio issues on pc) to Everyone : Does anyone know why all these processes have to be done in different organisms? Why could all these processes not be combined in a single cell?
10:32:52 From Alfred Spormann to Everyone : I think Bernhard will talk about this, or we can bring this question up later again. It’s a very good one!
10:33:29 From Daan de Groot (phone, audio issues on pc) to Everyone : Ok, I'll be patient then!
10:33:29 From Ramis Rafay to Everyone : Is acetate separated from fatty acids on that diagram because it is the pathway down to methane by acetoclastic methanogenesis or is it that eventually all fatty acids get degraded to acetate by secondary fermentation?
10:35:45 From Alfred Spormann to Everyone : There are many fermentations that produce acetate in addition to other  fatty acids. But acetate is very common. In fact, the most thermodynamically efficient fermentations produce more acetate.
10:36:34 From Ramis Rafay to Everyone : Thanks, Alfred!
10:37:29 From Seppe Kuehn to Everyone : Are these communities typically carbon limited?  Are N and P in excess somehow?
10:38:04 From Avi Flamholz to Everyone : depends on the environment as I understand
10:38:12 From Alfred Spormann to Everyone : Yap.
10:41:58 From Srividya Iyer-Biswas to Everyone : Followup to Daan de Groot’s question @1:32ET: In addition, are there fungi typically involved in these communities  (real world version) which are eliminated during lab culturing?
10:42:48 From Alfred Spormann to Everyone : Many fungi are not strictly anaerobic and can not grow over multiple generations anaerobically.
10:46:30 From David Ngugi to Everyone : Is hydrogen the single currency for most syntrophic interactions in nature? And is the second partner always a methanogen, or can hydrogen-oxidizers (Knall-gas bacteria) also contribute to the syntrophic process – if the forward reaction only requires removal of hydrogen to sufficient partial pressures.
10:47:46 From Alfred Spormann to Everyone : Formate is an equal interspecies electron transfer compound. Knall-gas bacteria would not work because they are aerobic and require O2, which would irreversibly inhibit the other partner.
10:51:53 From David Ngugi to Everyone : Thanks Alfred.
10:52:12 From Ramis Rafay to Everyone : How are we able to delineate specific electron transferring syntrophic partners existing in an undefined culture? Do we look for organisms whose metabolism forms the conditions for the other endergonic reactions to be feasible (such as lowering H2 partial pressure)?
10:55:08 From Avi Flamholz to Everyone : @ramis you can try to break the metabolism by poisoning one organism, for example, and see what happens to the community structure and metabolism
10:58:33 From Ramis Rafay to Everyone : @Avi, thanks. That is a good point. But wouldn't that require you to know whom to inhibit/poison specifically apriori?
10:58:43 From Hector Hernandez Gonzalez to Everyone : How difficult would it be for an organism to develop/perform the set of reactions that got lost in the community by the removal of the organism that perform that process in originally?
10:59:39 From Avi Flamholz to Everyone : @ramis, yes that’s just one kind of approach. for example, in our current era you can use sequencing to see which genes are present, see which species they are likely to come from, etc.
11:16:19 From Hülsmann Matthias to Everyone : the methane produced in sediments, does it usually gas out and enter the atmosphere, or is it rather oxidised as it diffuses into regions with higher oxygen availability?
11:17:09 From Alfred Spormann to Everyone : Often it is oxidized once methane gets into an environment with and electron acceptor; kinetically fastest with O2.
11:18:23 From Avi Flamholz to Everyone : was just in a talk about this yesterday, apparently it is often oxidized to CO2 when the leakage is slow (e.g. slow melting of permafrost) but can be leaked as CH4 when there is a faster release process (e.g. CH4 bubbles in arctic lakes)
11:20:53 From Hülsmann Matthias to Everyone : I see, thanks Alfred and Avi
11:29:13 From Avi Flamholz to Everyone : maybe when cells are energy limited maintaining a large genome and regulatory apparatus matters a lot more than it does in energy surfeit?
11:30:02 From Hector Hernandez Gonzalez to Everyone : Are methanogenic cells typically smaller than aerobe cells?
11:30:19 From Alfred Spormann to Everyone : Same order of magnitude
11:30:41 From Hector Hernandez Gonzalez to Everyone : Thanks Alfred
11:34:17 From Ramis Rafay to Everyone : But if their division rate is also codependent, would we necessarily see that sort of spatial partitioning occur?
11:35:07 From Wenying Shou to Everyone : We have written a paper on intermixed spatial organization of mutualistic communities. Andrew Murray lab also has a paper.https://elifesciences.org/articles/00960
11:35:48 From Wenying Shou to Everyone : sorry, it should be https://elifesciences.org/articles/00230
11:35:49 From Avi Flamholz to Everyone : @ramis there is a nice recent investigation of dependence of growth rate on spatial mixing in a synthetic symbiosis
11:36:14 From Avi Flamholz to Everyone : https://www.nature.com/articles/s41559-019-1080-2
11:37:12 From Ramis Rafay to Everyone : Thanks @Wenying and @Avi
11:37:18 From Avi Flamholz to Everyone : short answer — will depend on the balance of growth and diffusive rates. in the anaerobic system the growth is very slow, but H2 is a relatively fast-diffusing molecule
11:38:18 From Ramis Rafay to Everyone : I suppose the uptake/efflux rate of H2 is also relevant here but that is probably part of growth rate/stoichiometric differences?
11:40:30 From Avi Flamholz to Everyone : are these sediments always poor enough in terminal electron acceptors that making CH4 is the only option?
11:40:55 From Hülsmann Matthias to Everyone : I’m still very puzzled why a butyrate fermenting organism would not acquire methanogenesis to make use of its “waste hydrogen”… it seems to me the limited proteome explanation doesn’t work in that case
11:41:03 From Tingting Yang to Everyone : How much of the mixing "strategies" within different species could be related to the extracellular electron transport?
11:46:29 From Petra Steffen to Everyone : Question on the presentation: will there be a literature list at the end to read up on the different topics?
I am going to do research on very deep lacustrine sediments and I wonder if in this extremely energy limited environment syntrophic cooperations are found more often than in other environments. And if the organisms I might find there have particularly short metabolic pathways. I#m at the very beginning of my research.
11:48:31 From Rory Gordon to Everyone : The cytosol of the different bacteria may favour their respective roles in metabolism
11:48:42 From Hülsmann Matthias to Everyone : @ Avi - I guess the view is rather that sediments are so rich in organic material that even when all “good” electron acceptors are used up there is still more organic material to metabolise
11:50:24 From Ramis Rafay to Everyone : CH4 is also the sort of final frontier for carbon in terms of reduction, I think 
11:51:14 From Avi Flamholz to Everyone : @Matthias but surely there is a process depositing new mineral by sinking? I guess we are thinking about the deeper parts of the sediment where the e- acceptors are all used up
11:56:01 From Petra Steffen to Everyone : Another question: I'm confused, but maybe I have missunderstood something. In an earlier lecture Alfred talked about rate vs. yield trade-off. If I understood it right: when there is little flux and energy available the metabolic pathways will be longer, so that you get the highest yield out of the small flux. Yet, now, Bernhard connects energy limited environments to short pathways because it needs less enzymes and other stuff (sorry, I'm a little confused at the moment) for the cell to produce and sustain.
11:56:33 From Petra Steffen to Everyone : Am I on the wrong track or have an error in my thinking. Can someone resolve this?
11:58:20 From Alfred Spormann to Everyone : Petra, great questions of general interest! I suggest to bring this up in a discussion with Bernhard towards the end.
11:58:39 From Petra Steffen to Everyone : Okay, I will do that. Thanks.
13:04:03 From Petra Steffen to Everyone : Thank you very much for your input!
13:04:13 From Elisa Marquez Zavala to Everyone : Thank you!
13:04:17 From Miguel Alberto Pantoja Zepeda to Everyone : ty
13:04:24 From Malaika Ebert to Everyone : thank you for this great talk