ternary consortium does not have a dinitrogen flux

[djinnome]

Hi @mcnaughtonadm

The flux for EX_n2_e is zero in azotobacter for the ternary consortia.

Instead, it appears to be using $NO_3$ as the nitrogen source

Image thanks to @ShantMahserejian

[mcnaughtonadm]

Okay, looks like n2 isn't in the medium. Will rerun with it included.

[djinnome]

$N_2$ is expensive to consume. Might want to consider removing $NO_3$ from the media, too.

[djinnome]

Also just noticed that the medium appears to contain glc__D and leu__L and does not appear to need sucr__D
What changes to the consortia are needed to get it to grow using co2 and n2 as the only carbon and nitrogen sources?

[djinnome]

Hey @mcnaughtonadm thanks for pushing this task through to completion. When @ShantMahserejian has generated the new ternary alluvial diagram, we can close this issue

[mcnaughtonadm]

I ran the ternary under 2 new conditions:

1. With CO2 and N2 as the sole carbon and nitrogen sources provided in the combined media.
2. Same as 1. but with the photons reduced to only the 530 and 690 wavelengths. These are the only ""metabolites"" being used in FBA so this should clear some visual clutter of the alluvial.

1 -> ternary_model_co2_n2_growth.csv 2 -> ternary_model_co2_n2_growth_reduced_photons.csv

[mcnaughtonadm]

This growth condition can help center some of the model curation that needs to be done as this provides incomplete community growth as is.

[ShantMahserejian]

Here's the alluvial diagram for the updated model and fluxes.

• Note 1: The flux values have been log-log transformed to aid visualization
• Note 2: Andrew used two conditions to produce flux files, but both produced the same diagram results

[djinnome]

This is fabulous! At first I was a bit surprised, because it appeared as if Rhodo was fixing CO2 (which would be bad), but then I saw that what it actually appears to be doing is converting CO2 to HCO3 (which isn't perfect, but is not nearly as bad). Furthermore, it is clear that more CO2 is being consumed by Syn than is produced by Azo (which is good). Ideally, we would separate out CO2 so that there is the flux of CO2 that is coming from the media, and then there is the CO2 that is exchanged, but if you don't have time for that, I can always explain why what appears counterintuitive still makes sense during the poster session if there is time.

[djinnome]

• [ ] For @mcnaughtonadm create a source metabolite for co2 and h2o and o2
• [ ] For @ShantMahserejian create new source metabolites on the left-hand side of the alluvial diagram
• [ ] For @mcnaughtonadm remove the reaction that converts co2 to hco3 in rhodo and see if we can remove a confusing flux
• [ ] What happened to the excreted metabolites? Is this because there is no-growth?
• [ ] Should we have a flux for biomass (even though it isn't technically an exchange metabolite. It seems to be a good sink metabolite