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

Abstract 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. 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. 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. The results showed that 39 endophytic OTUs 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%) served as the dominant genera that coexisted in all the upland rice seeds tested and represent the core microbiota in upland rice seeds. 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. The results showed that 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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Composition and Diversity of Endophytic Bacterial Community in Seeds of Upland Rice Resources from Different Origin Habitats in Yunnan Province of China

10.21203/rs.3.rs-373041/v1 ◽

2021 ◽

Author(s):

Zhishan Wang ◽

Yongqiang Zhu ◽

Ni Li ◽

Biqi Sun ◽

Hai Liu ◽

...

Keyword(s):

Environmental Factors ◽

Bacterial Community ◽

Endophytic Bacteria ◽

Yunnan Province ◽

Upland Rice ◽

Population Increase ◽

Core Microbiota ◽

The Core ◽

Endophytic Bacterial Community ◽

Rice Seeds

Abstract 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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Diversity Analysis of Endophytic Bacterial Community in Two Citrus Cultivars With Different Resistance to Citrus Canker

10.21203/rs.3.rs-347972/v1 ◽

2021 ◽

Author(s):

Bing Liu ◽

Jiahao Lai ◽

Simeng Wu ◽

Junxi Jiang ◽

Weigang Kuang

Keyword(s):

Bacterial Community ◽

Endophytic Bacteria ◽

Citrus Canker ◽

Navel Orange ◽

Xanthomonas Citri ◽

Canker Disease ◽

Satsuma Mandarin ◽

Endophytic Bacterial Community ◽

Dominant Bacteria ◽

The Relationship

Abstract The selective infection of Xanthomonas citri pv. citri to citrus cultivars is universally known, but it is not clarified whether there is a relationship between endophytic bacteria and the resistance of host variety to canker disease. In order to explore the relationship, Satsuma mandarin and Newhall navel orange were collected respectively as samples of resistant or susceptible cultivars to citrus canker disease, and endophytic bacterial community of two citrus cultivars were analyzed by using a next-generation, Illumina-based sequencing approach. Simultaneously, the seasonal dynamics of endophytic bacterial community and dominant genera were analyzed. The results showed that there were four dominant groups including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes in all samples at phylum level. Endophytic bacteria were the most abundant in spring samples, then in summer and autumn samples. There were some differences between endophytic bacterial community of resistant citrus and that of susceptible citrus to canker disease, and the endophytic bacteria of Satsuma mandarin are more abundant than that of Newhall navel orange. According to the analysis of dominant bacteria in two citrus cultivars, it was found that some endophytic bacteria with antagonistic characteristics existed universally in all samples, although the dominant bacteria in different seasonal sample were different. However, in Newhall navel orange of susceptible citrus to canker disease, there were not only some bacteria against Xanthomonas citri pv. citri, but also some cooperative bacteria of canker occurrence like Stenotrophomonas.

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Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China

Microorganisms ◽

10.3390/microorganisms7020047 ◽

2019 ◽

Vol 7 (2) ◽

pp. 47 ◽

Cited By ~ 6

Author(s):

Zhen-Shan Deng ◽

Bao-Cheng Zhang ◽

Xiang-Ying Qi ◽

Zhi-Hong Sun ◽

Xiao-Long He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Endophytic Bacteria ◽

Growth Promotion ◽

Bacterial Community Composition ◽

Shannon Index ◽

Plant Production ◽

Total Carbon ◽

Shaanxi Province ◽

Endophytic Bacterial Community

Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.

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Insights into the Endophytic Bacterial Community Comparison and their Potential Role in the Dimorphic Seeds of Halophyte Suaeda Glauca

10.21203/rs.3.rs-153202/v1 ◽

2021 ◽

Author(s):

Hongfei Wang ◽

Manik Prabhu Narsing Rao ◽

Yanli Gao ◽

Xinyang Li ◽

Rui Gao ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Seed Coat ◽

Bacterial Communities ◽

Endophytic Bacteria ◽

Ecological Adaptation ◽

Endophytic Bacterial Community ◽

Suaeda Glauca ◽

Black Seeds ◽

Disturbed Environment

Abstract Background: The seed dimorphism was thought to be a bet-hedging strategy, which assists plants to survive in the disturbed environment and has been widely studied for their ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In the present study, we firstly used 16S rRNA high-throughput gene sequencing method to compare the bacterial diversity and community composition between brown and black seeds of Suaeda glauca. Results: A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e. pectinase, cellulolytic and xylanolytic activities). Conclusion: The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different bacterial function roles. The endophytic bacterial communities of the dimorphic seeds might be influenced mainly by the seed coat structure and partly by seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

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

10.21203/rs.3.rs-23885/v1 ◽

2020 ◽

Author(s):

Zhishan Wang ◽

Yongqiang Zhu ◽

Ruixue Jing ◽

Xianyu Wu ◽

Ni Li ◽

...

Keyword(s):

Community Structure ◽

High Throughput ◽

High Throughput Sequencing ◽

Upland Rice ◽

Functional Evaluation ◽

Soil Environment ◽

Soil Microbial Community Structure ◽

The Core ◽

Rice Seeds ◽

The Impact

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 re-action 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.

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Endogenous bacterial community structure of Pinus massoniana with differing resistance to pine wilt disease

Nematology ◽

10.1163/15685411-bja10081 ◽

2021 ◽

pp. 1-17

Author(s):

Wei Lu ◽

Xiao-Jia Zhao ◽

Jia-Jin Tan

Keyword(s):

Disease Resistance ◽

Bacterial Community ◽

Endophytic Bacteria ◽

Pine Wilt Disease ◽

Illumina Miseq ◽

Pinus Massoniana ◽

Wilt Disease ◽

Pine Wilt ◽

Disease Resistant ◽

Endophytic Bacterial Community

Summary Pine wilt disease (PWD) is a devastating pine disease caused by Bursaphelenchus xylophilus and its main host in China is Pinus massoniana. The relationship between endophytic bacteria and disease resistance in P. massoniana remains unclear. In this paper, the leaves, roots, stems and treetops of different disease-resistant P. massoniana were studied as the research objective and Illumina MiSeq sequencing was used to analyse whether there were significant differences in the composition and diversity of endophytic bacterial communities between different disease-resistant P. massoniana. The results showed that at the genus level there were no obvious differences in the composition of the endophytic bacterial community of different disease-resistant P. massoniana in the leaves, but there were obvious differences in the roots, stems and treetops. The richness and diversity of endophytic bacteria in P. massoniana had no significant impact on its disease resistance, whilst the structure of endophytic bacterial community in stems and treetops may be related to its disease resistance.

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Diversity of Cultivated Endophytic Bacteria from Sugarcane: Genetic and Biochemical Characterization of Burkholderia cepacia Complex Isolates

Applied and Environmental Microbiology ◽

10.1128/aem.01222-07 ◽

2007 ◽

Vol 73 (22) ◽

pp. 7259-7267 ◽

Cited By ~ 123

Author(s):

Rodrigo Mendes ◽

Aline A. Pizzirani-Kleiner ◽

Welington L. Araujo ◽

Jos M. Raaijmakers

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Burkholderia Cepacia ◽

Endophytic Bacteria ◽

Pathogenic Bacteria ◽

Biochemical Characterization ◽

Burkholderia Cepacia Complex ◽

Rrna Gene ◽

Endophytic Bacterial Community

ABSTRACT Bacteria were isolated from the rhizosphere and from inside the roots and stems of sugarcane plants grown in the field in Brazil. Endophytic bacteria were found in both the roots and the stems of sugarcane plants, with a significantly higher density in the roots. Many of the cultivated endophytic bacteria were shown to produce the plant growth hormone indoleacetic acid, and this trait was more frequently found among bacteria from the stem. 16S rRNA gene sequence analysis revealed that the selected isolates of the endophytic bacterial community of sugarcane belong to the genera of Burkholderia, Pantoea, Pseudomonas, and Microbacterium. Bacterial isolates belonging to the genus Burkholderia were the most predominant among the endophytic bacteria. Many of the Burkholderia isolates produced the antifungal metabolite pyrrolnitrin, and all were able to grow at 37°C. Phylogenetic analyses of the 16S rRNA gene and recA gene sequences indicated that the endophytic Burkholderia isolates from sugarcane are closely related to clinical isolates of the Burkholderia cepacia complex and clustered with B. cenocepacia (gv. III) isolates from cystic fibrosis patients. These results suggest that isolates of the B. cepacia complex are an integral part of the endophytic bacterial community of sugarcane in Brazil and reinforce the hypothesis that plant-associated environments may act as a niche for putative opportunistic human pathogenic bacteria.

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The Temporal Structure and Association Networks of Endophytic Bacteria in Pea Roots and Nodules

10.21203/rs.3.rs-315499/v1 ◽

2021 ◽

Author(s):

Xin Lv ◽

Qiankun Wang ◽

Xiaoyan Zhang ◽

Junjie Hao ◽

Li Li ◽

...

Keyword(s):

Life Cycle ◽

Bacterial Community ◽

Endophytic Bacteria ◽

Developmental Stages ◽

Temporal Structure ◽

Mature Stage ◽

Rrna Gene ◽

Plant Life ◽

Endophytic Bacterial Community ◽

Plant Life Cycle

Abstract Background and aims Endophytic bacteria from legume roots and nodules play important roles in regulating plant growth and health. However, little is known about how the endophytic bacteria community changes and how it interacts with each other throughout the plant life cycle. Methods We collected twenty pea cultivars to study the composition and structure of endophytic bacterial community during the whole developmental period using Illumina sequencing of 16S rRNA gene. Results Here we show that the development period significantly affected the structure of root endophytic bacterial community and peas recruit different root microbes during different developmental stages. The complexity of microbial community first increased and then decreased with the growth of pea. Rhizobium began to accumulate in pea seedling roots, and the content peaked at flowering stage and remained at high levels during the mature stage. In the flowering and mature stage, the relative abundance of Pseudomonas increased. Conclusions These findings can deepen the overall understanding of the community structure and interaction network of endophytic bacteria from pea root and nodules, and provide a detail for the establishment of root endophytic bacteria throughout the plant life cycle.

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Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year

BMC Microbiology ◽

10.1186/s12866-020-01977-3 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Hanli Dang ◽

Tao Zhang ◽

Guifang Li ◽

Yudi Mu ◽

Xinhua Lv ◽

...

Keyword(s):

Bacterial Community ◽

Bioactive Compounds ◽

Endophytic Bacteria ◽

Abiotic Factors ◽

Bacterial Community Composition ◽

Licorice Root ◽

Leaf Water Content ◽

Total Flavonoids ◽

Composition And Structure ◽

Endophytic Bacterial Community

Abstract Background The dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites. Results In this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1–3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1–3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium. Conclusions This study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.

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Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca

BMC Microbiology ◽

10.1186/s12866-021-02206-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Hongfei Wang ◽

Manik Prabhu Narsing Rao ◽

Yanli Gao ◽

Xinyang Li ◽

Rui Gao ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Seed Coat ◽

Bacterial Communities ◽

Endophytic Bacteria ◽

Ecological Adaptation ◽

Endophytic Bacterial Community ◽

Suaeda Glauca ◽

Black Seeds ◽

Disturbed Environment

Abstract Background Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. Results A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). Conclusion The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

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