Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures

Abstract

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.

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.