Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines

Liu, Yang; Xu, Pengpeng; Yang, Fuzhen; Li, Miao; Yan, Hai; Ni, Li; Zhang, Xiaoxia; Wang, Weiping

doi:10.1007/s10725-018-0467-4

Cited by 30 publications

(31 citation statements)

References 54 publications

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“…The major shared genera were Pantoea, Pseudomonas, Methylobacterium, Sphingomonas, Microbacterium, Aurantimonas, Agrobacterium, Curtobacterium, Erwinia, Buttiauxella and Magnetospirillum. Pantoea Microbacterium as endophytic dominant genera were also isolated or detected from seeds of rice, peanuts, browntop millet, Marama bean and so on (Liu et al 2019;Zhang et al 2018;Jiang et al 2013;Sobolev et al 2013;Verma and White 2018;Chimwamurombe et al 2016). It has been reported that many species of Pseudomonas, Sphingomonas and Microbacteriumcan promote plant growth by improving the nitrogen-fixing ability of plants or secreting secondary metabolites with antibacterial and plant growth benefits.…”

Section: Discussionmentioning

confidence: 99%

“…Firstly, the husks of each upland rice seed sample were removed by a small sheller. Then, under aseptic conditions the following operations were performed in the order listed: husked seeds were washed 3 times with prepared sterile water; 2.5 g of seeds were placed in a clean and sterile 50 mL tube containing 25 mL of phosphate buffer (per litre: 7.15 g of NaH 2 PO 4 •2H 2 O, 22.04 g of Na 2 HPO 4 •12H 2 O, 200 µL of Silwet L-77) (Zhang et al 2018;Liu et al 2019), and the seeds were sonicated twice by an Ultrasonic Processor Scientz-IID sonicator (NingBo Scientz Biotechnology Co., Ltd., China) at low power (237.5 W; 950 W×25%) in an ice bath for 5 min (alternating thirty 2-s bursts and thirty 2-s rests) (Lundberg et al 2012;Zhang et al 2018;Liu et al 2019). To validate that the surface was sterilized, sterile tweezers were used to press surface-sterilized seeds into LB medium (LUQIAO), and the samples were incubated at 30 °C for 72 h.…”

Section: Sample Surface Sterilization and Treatmentmentioning

confidence: 99%

“…Although researchers have done little research on the endophytes of upland rice seeds, the research on the endophytes of rice seeds is very mature. Liu et al (2019) used high-throughput sequencing technology to investigate the diversity and community structure of endophytic bacteria in super hybrid rice "Shenliangyou 5814" and its parents, and found that the dominant genus shared by the three are Pantoea, Methylobacterium, Sphingomonas, Rhizobium and Microbacterium and Pseudomonas. Zhang et al (2018) used the same method to explore five different genotypes of rice seeds, and the results showed that the common dominant genera were Pantoea, Acinetobacter, Xanthomonas, Bacillus, Flavobacterium, Stenotrophomonas, Neorhizobium and Pseudomonas.…”

Section: The Venn Diagram Data (Supplementarymentioning

confidence: 99%

“…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).…”

Section: The Venn Diagram Data (Supplementarymentioning

confidence: 99%

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

et al. 2020

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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...

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Section: Discussionmentioning

confidence: 99%

Section: Sample Surface Sterilization and Treatmentmentioning

confidence: 99%

Section: The Venn Diagram Data (Supplementarymentioning

confidence: 99%

Section: The Venn Diagram Data (Supplementarymentioning

confidence: 99%

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

et al. 2020

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“…Many studies have also found that the establishment of plant endophyte diversity and community structure is closely related to plant variety, genotype, growth environment and geographical location (Edwards et al 2015 Plant seed is not only the reproductive organ of the plant, the preserver and transmitter of plant genetic information, but also the adaptive strategy to ensure species reproduction under stress, which is of great signi cance to plant reproduction and agricultural production (Steinbrecher and Leubner-Metzger 2017; Domergue et al 2019). Studies have shown that plant seeds are rich in microbial resources, which are the transmission medium of microorganisms from maternal plants in offspring plants, and are responsible for passing bene cial microorganisms from generation to generation, and then achieve a direct or indirect impact on plant growth and development, health, quality, yield and functional components and other biological characteristics (Walitang et al 2018a; Berg and Raaijmakers 2018;Li et al 2019a;Liu et al 2019). Endophytic bacteria are the most easily identi ed microorganisms by researchers.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Zhu

et al. 2021

Preprint

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Upland rice has the characteristics of strong drought tolerance and wide adaptability. Cultivating upland rice with high yield and high quality can solve the contradiction between food shortage, water shortage, and population increase in countries all over the world, and is of great significance to the sustainable development of agriculture. This study aims to reveal the "core microbiota" of the endophytic bacteria in upland rice seeds in the Yunnan Province of China by examining their diversity and community structures. Through the correlation analysis with upland rice habitat environmental factors, the effects of climate and altitude on the structure and diversity of endophytic bacterial community in upland rice seeds were further revealed. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to investigate the structure and diversity of endophytic bacterial communities using 12 upland rice variety seeds from different areas in Yunnan Province of China as materials. Here, 39 endophytic OTUs (0.68%) were found to coexist in all samples. At the phylum level, the first dominant phyla in the 12 seed samples were Proteobacteria (66.92–99.98%). At the genus level, Pantoea (9.75–99.24%), Pseudomonas (0.11–37.24%), Curtobacterium (0.01–19.90%), Microbacterium (0.01–14.95%), Methylobacterium (0.40–5.86%), Agrobacterium (0.01–4.53%), Sphingomonas (0.04–1.56%), Aurantimonas (0.01–1.45%) and Rhodococcus (0.11–1.09%), which represent the core microbiota in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. Environmental factors such as temperature, precipitation and altitude have great influences on the structure of endophytic bacterial community in upland rice seeds. This study is of great significance to explore the relationship between upland rice and its endophytic bacteria and to tap the resources of drought-tolerant bacteria to improve the yield of local upland rice.

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Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species, Capsella bursa‐pastoris

Choi

Jeong

Kim

2022

Ecology and Evolution

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Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa ‐ pastoris , a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth‐promoting traits. Actinobacteria, Firmicutes, Alpha‐, and Gammaproteobacteria were major bacterial phyla inside seeds. C . bursa ‐ pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera ( Bacillus , Rhodococcus , Streptomyces , Staphylococcus , Paenibacillus , Pseudomonas ) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth‐promoting traits like phosphate solubilization activity, indole‐3‐acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C . bursa ‐ pastoris or its close relative A . thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C . bursa ‐ pastoris , contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.

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Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines

Cited by 30 publications

References 54 publications

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

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

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

Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species, Capsella bursa‐pastoris

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