Fig 1.
Wild rice (Oryza longistaminata) plant and rhizome.
(A) Plants with strong rhizomes. Scale bar: 2 cm. (B) Rhizome and rhizome apical tips with sheath. Scale bar: 1 cm. (C-D) The vertical-section of the root apical tip. Scale bar: 160 and 40 μm. (E-F) The vertical-section of the rhizome apical tip. Scale bar: 160 and 40 μm.
Fig 2.
Microbiome alpha- and beta-diversity estimates.
(A) Species richness estimates (Chao and richness) and diversity indices (Shannon and Simpson) for the 48 samples from roots, rhizomes, stems, and leaves of O. longistaminata. (B-E) Unconstrained principal coordinate analyses (PCoAs) of microbial community composition among four different compartments of Oryza longistaminata at the ASV level based on the unweighted UniFrac (UUF), weighted UniFrac (WUF), Bray-Curtis and Jaccard distance matrix. (F-G) PCoAs and CAP of microbial community composition among three different compartments of Oryza longistaminata at the ASV level based on the Bray-Curtis distance matrix.
Fig 3.
ASV co-occurrence network interactions of leaves, roots, stems and rhizomes.
Co-occurrence relationships with strong Spearman’s correlation values (P-value < 0.5 and abs(r) > 0.6) are depicted for each compartment. The nodes represented unique ASV in the data sets.
Fig 4.
Distinctive taxa of the different compartments.
(A) Numbers of differentially ASVs among each compartment in Sankey diagram. (B) Feature table heatmap of distinctive taxa in different compartments using random forest analysis. Methanotrophs are labeled by red stars.
Fig 5.
Phylogenetic community structure of Oryza longistaminata.
PD, phylogenetic diversity; pd.obs.z, the standard effective size of phylogenetic diversity; mpd.obs.z, the standard effect size of mean pairwise distance among distinct taxa; mntd.obs.z, the standard effective size of mean nearest taxon distance among distinct taxa.
Fig 6.
Microbiota diversity, community structure and functional analysis between the roots and bulk soil.
(A) Alpha diversity estimates. (B) Beta diversity estimates. (C) ASVs involved in potential ecologically functions in roots and bulk soil. (D) ASVs involved in the potential CH4–N cycle between roots and bulk soil. Statistical significance was identified by the wilcoxon test with a false discovery rate (FDR)-corrected pairwise P values.