Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties

Abstract

The endophytic bacterial communities of the three most important rice varieties cultivated in Uruguay were compared by a multiphasic approach. Leaves of mature plants grown in field experiments for two consecutive crop seasons were studied. No significant differences were found in the heterotrophic bacterial density for the three varieties. Pantoea ananatis and Pseudomonas syringae constituted 51% of the total of the isolates. These species were always present regardless of the variety or the season. Molecular analysis based on the 16S rRNA gene was performed by terminal restriction fragment length polymorphism (T-RFLP) and cloning. T-RFLP analysis revealed that bacterial communities grouped according to the variety, although the three varieties presented communities that showed 74% or higher similarities. Brevundimonas, the dominant genus in the clone library (18% of the clones), which might be present in all varieties according to T-RFLP profiles, was not recovered by cultivation. Conversely, bacteria from the genus Pseudomonas were not detected in the clone library. These results indicate that communities established in leaves of physiologically different rice varieties were highly similar and composed by a reduced group of strongly associated and persistent bacteria that were partially recovered by cultivation.

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

“…In all the three stages of growth the root tissues were most colonized yielding the largest number of culturable bacteria (from 10 6 to 10 7 cfu gm −1 ). These bacterial counts are comparable to the ones obtained in other studies which have resulted in the isolation of endophytes from rice (Gyaneshwar et al ., ; Ferrando et al ., ).…”

Conservation and transmission of seed bacterial endophytes across generations following crossbreeding and repeated inbreeding of rice at different geographic locations

“…Pantoea ananatis (also the same bacterial identity in the previous study), Pseudomonas syringae and Brevundimonas sp. were also found to be potential core endophytes of rice and are mainly prominent in the leaves (Ferrando, Mañay, & Scavino, ). Clostridium and Paenibacillus were core endophytes of Zea while Enterobacter , Methylobacteria , Pantoea , and Pseudomonas were also found to be widespread among Zea cultivars (Johnston‐Monje & Raizada, ).…”

The communities of tomato (Solanum lycopersicumL.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing

“…Thus, the diversity of leaf endophytic bacteria and their beneficial effects on plant hosts is far from being well known. In the recent years, culture‐independent methods for DNA analysis contributed to gain insight into the composition of endophytic communities in leaves of different rice ( Oryza sativa ) varieties (Ferrando et al ., ) and several plant species naturally grown in the Tallgrass Prairie Preserve in Osage County (Oklahoma; Ding et al ., ), as well as in different organs of Styrian oil pumpkin ( Cucurbita pepo L. ssp. pepo var.…”