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

Abstract

There are comparatively diverse bacterial communities inside seeds, which are vertically transmitted and conserved, becoming sources of endophytes in the next generation of host plants. We studied how rice seed endophyte composition changed over time following crossbreeding, repeated inbreeding, subsequent human selection and planting of different rice seeds in different ecogeographical locations. Using terminal-restriction fragment length polymorphism analysis to study bacterial communities, we observed that diversity between the original parents and their offspring may show significant differences in richness, evenness and diversity indices. Heat maps reveal substantial contributions of both or either parent in the shaping of the bacterial seed endophytes of the offspring. Most of the terminal restriction fragments (T-RFs) of the subsequent progeny could be traced to any or both of its parents while unique T-RFs of the offspring suggest external sources of colonization particularly when the seeds were cultivated in different locations. Many similar groups of endophytic bacteria persist in the seeds even after recultivation in different locations, indicating resilience to environmental changes and conservation of bacteria across generations. This study suggests that parent plants contributed to the shaping of seed bacterial endophytes of their offspring, although it is also possible that these soil grown rice plants recruit similar populations of endophytes from the soil generation after generation. This study also highlights some bacterial groups belonging to Herbaspirillum, Microbacterium, Curtobacterium, Stenotrophomonas, Xanthomonas and Enterobacter that may be part of a transmitted and conserved "core microbiota" that are ubiquitous and dominant members of the endophytic communities of the rice seeds.

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

“…Geographical signatures are major shaping factors of bacterial communities of grape [52]. However, bacterial communities associated with surface-sterilized seeds of maize, rice, and pumpkin were more affected by plant genotypes than geographical factors [53][54][55][56]. We found that the effect of domestication exceeded that of geographical locations in variations of seed microbial communities.…”

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

“…Then, as the seed of one of the important organs of the plant and an important source of endophytes, where does its endophytes come from? A large number of studies have shown that the community assembly of seed endophytic bacteria may be affected by its parent, and that plants can autonomously select endophytic bacteria and spread them to the offspring through seeds (Liu et al 2019;Liu et al 2020;Walitang et al 2018;Truyens et al 2015). In addition, there are related studies that show that the the bacterial community in the soil environment can affect the composition of endogenous bacterial communities in other organs of the plant by affecting the microbial composition of the plant rhizosphere (Yang et al 2017;Haruna et al 2018).…”

Experimental Evidence of Microbial Inheritance in Plants and Transmission Routes from Seed to Phyllosphere and Root

“…Hodgson et al (2014) identi ed two fungal species in pollen, seed, and leaves of forbs grown in sterile conditions [13]. Walitang and coworkers (2019) reported several bacterial endophytes to be present in both rice seed and leaves [26].…”

“…Given the structural and chemical differences that exist between seed embryo and pericarp, we expected to nd spatial compartmentalization of the microbial community between the two tissues [19]. We also hypothesized that the majority of seed-associated microbes would be transient and that only a small fraction of the microbial taxa would be transmitted to the developing seedling [13,26]. We lacked a strong prior on the subsequent distribution of the transmitted microbiome, but some studies have suggested that the composition of seed-associated microorganisms re ects the microbial community in the roots [4,28], while seed transmission to the phyllosphere is more limited [29,30].…”