Endophytic bacteria are considered to originate from the external environment. To examine the hypothesis that rice (Oryza sativa, cultivar Kinuhikari) seeds are a source of endophytic bacteria, we isolated endophytic bacteria from the shoots, remains of the seeds, and roots of rice seedlings that were aseptically cultivated in vitro from surface-disinfected seeds. Of the various bacterial strains isolated, the closest relatives, identified by 16S rRNA gene sequencing, were: Bacillus firmus, B. fusiformis, B. pumilus, Caulobacter crescentus, Kocuria palustris, Micrococcus luteus, Methylobacterium fujisawaense, Me. radiotolerans, and Pantoea ananatis. The latter three species have been detected frequently inside both rice seedlings and mature rice plants. These results indicate that rice seeds are an important source of endophytic bacteria. The bacteria that colonize the seed interior appear to infect the subsequent generation via rice seeds and become the dominant endophytic species in the mature plant.

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.

The culturable endophytic bacteria in the leaves and roots of rice plants (Oryza sativa, cultivar Kinuhikari) cultivated on an experimental plot adjacent to a paddy field were studied during the maturation process, and a comparison with the bacteria inside rice seeds reported in a previous study was conducted. Culturable epiphytic bacteria were also isolated from the leaves and compared with the endophytic bacteria. The isolates were identified based on their 16S rRNA gene sequences. Many endophytes closely related to Bacillus, Curtobacterium, Methylobacterium, Sphingomonas and Pantoea from the leaves, and to Bacillus, Brevibacillus, Mycobacterium, Enterobacter, and Chryseobacterium from the roots were isolated. The endophytic bacterial flora of the leaves was similar to that of the seeds, but differed from that of the roots. As the rice plant matured, the ratio of Gram-negative strains among the isolates increased in the leaves (the isolates related to Curtobacterium decreased in number and those related to Methylobacterium and Pantoea increased), whereas the ratio of Gram-negative strains decreased in the roots (the isolates related to the order Rhizobiales decreased in number and were replaced by strains related to Bacillus and Brevibacillus capable of forming endospores). The isolates from the inside and surface of the leaf were closely related to 13 and 19 species, respectively. Among these isolates, the following 6 species related to Bacillus pumilus, Curtobacterium citreum (or C. flaccumfaciens, C. pusillum as the closest species), Methylobacterium aquaticum, Methylobacterium fujisawaense (or M. radiotolerans), Sphingomonas melonis and Sphingomonas yabuuchiae were common to both sites and constituted the majority at both sites.

Endophytic bacteria in the seeds of rice plants (Oryza sativa, cultivar Nipponbare) were studied during the rice maturation process by comparing them with the bacteria at the surface of rice seeds. The endophytic and surface bacteria were isolated from cultivated rice seeds by using a nutrient broth (NB) and a diluted nutrient broth (DNB) agar medium. The endophytes at the early stages of maturation were relatively diverse, consisting of strains closely related to the genera Bacillus, Sphingomonas and Pantoea. In contrast, the endophytic and surface bacteria at the middle and late stages of the maturation process (39 strains altogether) were all closely related only to the genus Bacillus with the exception of one isolate, and almost all of these strains were motile and spore-forming. It was deduced that these bacteria might have migrated into the rice seeds before they hardened that is, during the early stage (the endophytes at the early stage were also all motile and about half of them were spore-forming), subsisting as endospores during the middle and late stages of the maturation process. Furthermore, most of the isolates (19 of 23) from the surface bacteria and the endophytic bacteria grew better when sucrose (1.2 M) was added to the NB liquid medium. These bacteria may be able to adapt to a high osmotic pressure.