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

Abstract

Upland rice is an ecotype crop formed by long-term domestication and evolution of rice in the dry land without water layer. Generally, its stem and leaf are thick and luxuriant, its leaf is wide and light, its root system is developed, its root hair is abundant, its osmotic pressure of root and cell juice concentration of leaf are high, and it is drought resistant, heat-resistant and water absorbing. The purpose of this study is to reveal the "core flora" of endophytes in upland rice seeds by studying the diversity and community structure of endophytes in upland rice seeds, and to reveal the impact of soil environment on the formation of endophyte community structure in upland rice seeds by comparing with soil environment microorganisms in upland rice habitats. In this study, the high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to study the structure and diversity of endophytic bacterial communities using upland rice varieties collected in different places and soil samples from their unified planting sites as materials. There are 42 endophytic OTUs coexisted in the 14 samples. At the phylum level, the first dominant phyla was Proteobacteria (93.81-99.99%) in all 14 samples. At the genus level, Pantoea (8.77%-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which are probably the core microflora in upland rice seeds, served as the dominant genera that coexisted in all upland rice seeds tested. Compared with the soil microbial community structure in the upland rice uniform planting site, it was found that it had little effect on the endophytic community structure in upland rice seeds. This study is of great significance for the isolation, screening, functional evaluation and reaction of some functional microorganisms in upland rice in order to improve its agronomic traits. It also provides a certain reference for the interaction between microorganisms and plants. the adjacent plant tissues. Therefore, endophytes are ubiquitous in the plant host, including the aboveground and underground parts of the plant, even seeds, thus having a positive impact on the plant development (Zinniel et al. 2015; Chebotar et al. 2015). Endophytes can provide a variety of benefits to host plants, especially through multiple functions to improve the growth and health of plants, so that they can be protected from pathogens (Agler et al. 2016; Liu et al. 2017a,b; Xu et al. 2019; Afzal et al. 2019; Sánchez-Cruz et al. 2019). Under different environmental conditions, the communication and interaction between endophyte and plant is stronger than that between rhizosphere bacteria (Coutinho et al. 2015). A number of studies have shown that plant varieties, genotypes and geographical location have a great impact on the establishment of microbial diversity and community structure in plants (Liu et al. 2017a, 2019; Edwards et al. 2015). Although endophyte was discovered more than 100 years ago, its existe...

Composition and Diversity Of Endophytic Bacterial Community in Seeds of Upland Rice Resources from Different Origin Habitats in China

“…A large number of studies on the community structure and diversity of endophytic bacteria in plant seeds have also found that although there are coexisting endophytic dominant bacterial groups among different varieties of plant seeds, at the same time, they have signi cant differences in endophytic bacterial community structure and diversity (Xu et 2019). Although some studies have found that the endophytic bacterial community structure and diversity among different varieties of seeds are very similar, there are still some differences in the abundance of bacterial groups (Zhang et al 2018b;Wang et al 2020). However, there are no signi cant differences in endophytic bacterial diversity and community structure in some upland rice seeds, and they are particularly close in PCoA and NMDS results (Fig.…”

“…Studies on the root microbial diversity of upland rice and its effects on the growth and drought tolerance of upland rice have also been reported (Pang et al 2020). Our research group also explored the diversity and community structure of endophytic bacteria in upland rice seeds in different regions of China and preliminarily revealed the core microbiota of endophytic bacteria in upland rice seeds (Wang et al 2020).…”

“…In addition to these technologies, high-throughput sequencing has gradually become a new method to evaluate and analyze the diversity and community structure of endophytes in plant seeds. In the previous research, the undergraduate research group also used high-throughput sequencing technology to explore the endophytic bacterial diversity and community structure of 14 upland rice seeds collected in different areas of China (Wang et al 2020). However, compared with other plant tissue microorganisms, research on plant seed endophytes is still very limited, in particular, there are few studies on the effects of environmental factors related to plant growth on the diversity and community structure of endophytic bacteria in their seeds.…”

Endophytic Microbes Are Tools to Increase Tolerance in Jasione Plants Against Arsenic Stress

“…Therefore, a better starting point to obtain plant microbes would be to focus on the study of the seed endomicrobiota (Matsumoto et al, 2021;Moreira et al, 2021); this especially since they are selected generation to generation for the ability to enter the host plant (Hardoim et al, 2008). Nevertheless, seeds have already shown to be a microbiota reservoir providing beneficial traits to the host plant (Ewald, 1987;Rudgers et al, 2009;Hardoim, 2019;Wang et al, 2021). Jasione persistent OTUs were genera Pseudomonas spp., Ralstonia spp., Undibacterium spp., Cutibacterium spp., and Kocuria spp.…”

“…are common plant endophytes (Compant et al, 2011;Pacifico et al, 2019;Wang et al, 2021), acting also as biocontrol agents (Munakata et al, 2020) and members of the core microbiome of many plant species, including canola (Brassica napus) (Moreira et al, 2021). Recently, Pseudomonas has been found in rice plants with the ability to decrease arsenic translocation from roots into grains (Dolphen and Thiravetyan, 2019;Wang et al, 2021), and in lettuce roots as rare microbiota that protect against plant pathogens (Cardinale et al, 2015). Accordingly, other PGPB species, including Cutibacterium spp., identified in wheat (Triticum) seeds (Kuźniar et al, 2020;Abdullaeva et al, 2020); Undibacteriumin spp.…”