Endophytic bacterial communities in wild rice (Oryza officinalis) and their plant growth-promoting effects on perennial rice

Abstract

Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of O. officinalis were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from O. officinalis tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including Desulfomonile and Ruminiclostridium for roots; Lactobacillus, Acinetobacter, Cutibacterium and Dechloromonas for stems; and Stenotrophomonas, Chryseobacterium, Achromobacter and Methylobacterium for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from O. officinalis. Among them, 11 strains identified as Enterobacter mori, E. ludwigii, E. cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae and Kosakonia oryzae were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of O. officinalis and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.

Analysis of Bioactive Secondary Metabolites Produced by Endophytic Bacillus amyloliquefaciens against Rice Sheath Blight Pathogen Rhizoctonia solani

“…Further, endophytic bacterial strain B. amyloliquefaciens B6 isolated from O. officinalis was tested for its antagonistic activity against the pathogen under in vitro conditions. Similarly, Tian et al, (2023) isolated a total of 96 endophytic bacterial strains from O. officinalis, of which 11 strains performed promising PGP traits on perennial rice seedlings. These 11 strains belonging to the Enterobacter, Bacillus, Pseudomonas and Kosakonia species were reported to have utilization potential as biofertilizers for the sustained productivity of perennial rice.…”

“…One Gram-positive endophytic bacterial strain, Bacillus amyloliquefaciens B6 (GenBank accession no. OQ943610.1), isolated from leaves of Oryzae officinalis was used for the present study (Tian et al, 2023).…”

Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes

“…Endophytic microbes colonize the plant endophytic compartment and considerably influence plants’ growth, development, nutrition, and resistance to pathogens [ 1 , 2 , 3 , 4 , 5 ]. In plants, microbial diversity varies across different niches, with the endophytic microbiome of plant roots being primarily absorbed from the soil and transported to the stems and leaves through extracellular vesicles in the xylem vessels [ 6 , 7 ].…”

Biological control of Magnaporthe oryzae using natively isolated Bacillus subtilis G5 from Oryza officinalis roots

“…is known to have endured a variety of harsh conditions and natural calamities over a long period of time, making it a valuable genetic resource for rice breeding (Tan et al, 2004 ; Devanna et al, 2014 ). It also harbors a special and effective microbial community ecosystem, which is an ideal source of endophytes for the biocontrol of rice diseases (Tian et al, 2023 ). Moreover, compared with cultivated rice endophytes and rhizosphere bacteria, there are few studies on wild rice.…”