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cmsantosm / RiceMbiomeResponse

Processed data and R notebooks to reproduce analyses from our publication "Acquisition of a complex root microbiome reshapes the transcriptional landscape of rice plants"
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Experiment design about this study #1

Closed Kaoping closed 2 years ago

Kaoping commented 2 years ago

Hi Christian,

Recently I read you paper "Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants", it's really an excellent story. I am curious about two things:(1) why you set up the potted-soil plant controls ? If this potted-soil plant treatments mean you added soil rather than soil suspension after 7 germination? Because I think adding soil and adding soil suspension are the same treatment in this study. I am not sure I understand that correctly. (2) I recognized you picked out the core OTUs, but I can't find out how you defined the OTU is core OTU.

Thanks for your time. Best, Kaoping

cmsantosm commented 2 years ago

Hi Kaoping,

Thanks for your questions:

1) The soil-grown potted plants are very different from the soil-inoculated plants grown in semi-hydroponic containers. For the soil-grown controls, we transplanted 7-day-old axenic seedlings to potted agricultural soils and profiled their microbiomes 14 days post-transplantation. For soil-inoculated plants, we grew rice seedlings in closed sterile containers holding calcined clay and plant-growth media. The 7-day-old seedlings were inoculated with a diluted soil slurry derived from the same soils used for the soil-grown controls.

2) You can find the core OTU analysis in the mbiome_soil_diff.Rmd notebook (lines 126-193)

Kaoping commented 2 years ago

Thank you for the helpful explanation. This makes a lot more sense to me now.