Fig 1.
Phylogeny of 3,894 rumen bacterial OTU.
Branch lengths represent substitution number per site calculated by FastTree2[81]. Heritability estimates (h2) for each OTU abundance are plotted with a horizontal bar and colored by taxonomic group classification.
Fig 2.
Phylogeny of 189 rumen archaeal OTU abundance.
Branch lengths represent substitution number per site calculated by FastTree2[81]. Heritability estimates (h2) for each OTU abundance is plotted with a horizontal bar and colored by taxonomic group classification.
Table 1.
Estimated heritability (h2) and P-value for the relative abundances of bacterial and archaeal genera.
Fig 3.
Manhattan plot of rumen bacterial and archaeal genera associations with methane emissions (g/day) colored by heritability (h2) estimates.
Color gradient indicates genera h2 with light blue (h2 = 0) ranging to dark blue (h2 = 0.30). The y-axis is -log10(P) for association tests. The horizontal line represents the Benjamini-Hochberg FDR 15% for multiple testing significance thresholds. Genera above the threshold are a) Unclassified BS11 group; b) Sporobacter; c) Unclassified Victivallaceae; d) Unclassified Lentisphaeria; e) Unclassified Alphaproteobacteria; f) Unclassified Rickettsiales; and g) Sphaerochaeta.
Fig 4.
Principal coordinate analysis (PCoA) of rumen bacterial community diversity (a) and archaeal community diversity (b) based on 16S rRNA amplicon sequencing contrasting 10% highest methane emitters (orange), 10% lowest methane emitters (blue), and 80% intermediate emitters (grey). Distribution of high and low emitters along PCo1 showed significant differences (P < 0.001) for both figures.
Fig 5.
Proportion of variance in CH4 explained by different sources (Intra-class correlation coefficients, ICC) due to additive genetic effects (heritability) and rumen microbe content (microbiability), with respective standard errors when fit separately or jointly.