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.

Physiology of Methylotrophs Living in the Phyllosphere

“…In addition to methanol, plants emit methane, which is anaerobically generated by methanogens in soil via their aerenchyma, although some plants aerobically produce methane, which is assumed to be formed during the synthesis of pectin methyl ester groups coupled with photosynthesis [20,21]. Methane-utilizing methylotrophs, known as methanotrophs, also colonize the surface of plants [22][23][24][25][26]. Methane-and methanolutilizing methylotrophs inhabit various environments in nature besides the phyllosphere, and play important roles in the global carbon circulation of two major greenhouse gases, methane and CO 2 .…”

Favorable QTLs from Oryza longistaminata improve rice drought resistance

“…The genus Oryza consists of cultivated species, O. sativa and O. glaberrima , and 22 wild species including Oryza longistaminata. Wild rice species are known to possess many valuable genes that do not exist in cultivated rice varieties [ 10 ]. However, only a few works regarding the cloning and QTLs mapping of valuable genes from wild rice species have been reported, systematically evaluation of wild rice and its derivative populations should be a priority in rice breeding programs.…”

“…Oryza longistaminata , an Africa wild rice, which is suggested as the ancient ancestor of cultivated rice, has numerous interesting traits, such as long stigma and large anthers, and high resistance to abiotic and biotic stresses including drought tolerance and bacterial blight resistance [ 10 ]. Precise and effective exploitation of the hidden valuable genes within O. longistaminata will help to ensure sustainable rice production and global food security in the ever-changing climatic conditions.…”

Solation and Characterization of Putative Nitrogen-Fixing Endophytes from Three Distinct Wild Rice Species in Sri Lanka

“…In recent times, the bacterial endophytes of the rhizome of the wild and perennial rice species, Oryza longistaminata, were identified by 16s rDNA sequencing as belonging to the genera, Streptococcus, Bacillus, and Methylobacterium (Peng et al, 2021). Especially the availability of members of Methylobacteriaceae in the rhizome, was significantly higher compared to the leaf and root (Peng et al, 2021).…”

“…In recent times, the bacterial endophytes of the rhizome of the wild and perennial rice species, Oryza longistaminata, were identified by 16s rDNA sequencing as belonging to the genera, Streptococcus, Bacillus, and Methylobacterium (Peng et al, 2021). Especially the availability of members of Methylobacteriaceae in the rhizome, was significantly higher compared to the leaf and root (Peng et al, 2021). Another nitrogen fixer from Oryza latifolia, Kosakonia oryzae type strain Ola 51 T , of which the genome was sequenced, was identified as a plant growth promoting bacterium due to the availability of auxin producing genes, while also containing both the nif and anf gene clusters for nitrogen fixation (Li et al, 2017).…”