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Fig. 3 | Microbiome

Fig. 3

From: HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Fig. 3

13C-Hyphosphere metagenome-assembled genomes (MAGs) isolated by SIP metagenomics. Fraction DNA mass (ng) versus fraction density for A total DNA that was fractionated from 13C-AMF DNA (red lines) and 12C-AMF control DNA (blue lines); n=3. Dashed lines are the weighted average density (WAD) of the DNA from the 13C and 12C replicate gradients. Within each gradient, we used qSIP to estimate taxon-specific DNA masses for B the AMF host Rhizophagus intraradices, and all MAGs. C A Myxococcota MAG (Fen-1088 mCT241) was the most 13C-enriched MAG detected, and D an archaeal ammonia oxidizer (Nitrososphaera mCT2) was among the most 13C-enriched MAGs detected. Taxon-specific DNA masses were estimated by multiplying a fraction’s total DNA mass by taxon relative abundance (i.e., MAG counts divided by metagenomic library counts). E To isolate hyphosphere soil from the influence of roots, we used a two-compartment experimental microcosm where Avena barbata inoculated with AMF grew in one compartment, and AMF hyphae (pink lines) crossed an air gap to access soil in the no-plant compartment; soil aggregates with visible hyphae were collected from this compartment for SIP (see Supplemental Figure S2 for detailed experimental design). F We calculated the estimated median atom percent excess (APE) for all assembled MAGs, where red bars indicate the 212 13C-hyphosphere MAGs with detectable isotopic enrichment (lower 90% CI bound greater than 0% APE-13C), and blue bars indicate 87 bulk soil MAGs that were unenriched (lower 90% CI bound below 0% APE-13C); error bars are suppressed for readability. MAGs are grouped by phylum, and letters indicate the APE of the taxa shown in panels B–D. The dashed gray line indicates the APE of the AMF, which supplied 13C to the no-plant compartment. Inset diagram (E) modified with permission from Kakouridis et al. [41]

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