scholarly journals The Dynamics of Endophytic Bacterial Community Structure in Rice Roots under Different Field Management Systems

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1623
Author(s):  
Guan-Ying Lin ◽  
Chia-Yu Lin ◽  
Su-Jein Chang ◽  
Wei-Yi Lin
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Endophytic Bacteria ◽  
Growth Stage ◽  
Bacterial Community Composition ◽  
Farming Systems ◽  
Rrna Gene ◽  
Rice Roots ◽  
Field Management ◽  
Endophytic Bacterial Community

The structure of endophytic bacteria is important to plant health and stress tolerance, but little is known about the impacts of farming systems on temporal changes in diversity of endophytic bacteria. In this study, we investigated the endophytic microbiome in rice roots under organic and conventional farming systems at the seedling and tillering stages over two consecutive cropping seasons using 16S rRNA gene sequencing. Although the composition of the microbiome was significantly influenced by a field management system, growth stage, and interaction between the two factors, the growth stage alone explained more than 40% of variance. Soil pH and organic matter content also partially influenced the endophytic bacterial community composition. In addition, through indicator species analysis and the functional profiles predicted by phylogenetic analysis, we revealed the selection force of rice roots at the tillering stage to recruit endophytes, which are beneficial to plant growth. In summary, our data show that the dynamics of rice root bacterial composition are mainly influenced by the plant growth stage. Our findings offer new insights regarding the control of the root microbiome by host plants and the influence of farming systems.

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

2019 ◽  
Vol 7 (2) ◽  
pp. 47 ◽  
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.

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

2007 ◽  
Vol 73 (22) ◽  
pp. 7259-7267 ◽  
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.

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

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.

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

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.

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

2020 ◽  
Author(s):  
Hanli Dang ◽  
Tao Zhang ◽  
Guifang Li ◽  
Yudi Mu ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Endophytic Bacteria ◽  
Abiotic Factors ◽  
Bacterial Community Composition ◽  
Licorice Root ◽  
Leaf Water Content ◽  
Total Flavonoids ◽  
Effective Components ◽  
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, the activities of which are attributed to a variety of effective components 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 effective components (glycyrrhizic acid, liquiritin and total flavonoids) in different varieties of medicinal licorices (Glycyrrhiza uralensis Fisch., Glycyrrhiza glabra L.and Glycyrrhiza inflata Batal.) and in different planting years (1–3 years). Our results showed that the contents of the effective components in the roots of medicinal licorices were not affected by the variety, but were significantly affected by the 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, 73,316 effective sequences with an average length of 372 nucleotides (nt) were obtained after quality control, and 2,432 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 structure of endophytic bacteria and effective components, which provides a reference for improving the quality of licorice.

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

2020 ◽  
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 2,432 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.

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

Assessing the Plant Growth-promoting Traits and Host Specificity of Endophytic Bacteria of Pulse Crops

2021 ◽  
Author(s):  
R. Thamizh Vendan ◽  
D. Balachandar
Keyword(s):  
Plant Growth ◽  
Endophytic Bacteria ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Growth And Yield ◽  
Rrna Gene ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Rrna Gene Sequencing ◽  
Plant Growth Promoting Traits

Background: Symbiotic associations between legumes and Rhizobia are ancient and fundamental. However, the plant growth-promoting endophytes other than Rhizobia are not yet fully explored for pulses productivity. The present study was aimed to isolate efficient endophytic bacteria from pulses, assess their diversity, screen their plant growth-promoting activities and to test their potential as bio inoculants for pulses.Methods: We have isolated several endophytic bacteria from pulse crops more specifically from blackgram (Vigna mungo) and greengram (Vigna radiata). After careful screening, 15 promising endophytic isolates were selected for this study. The identification of endophytic bacterial isolates was performed by 16S rRNA gene sequencing. The isolates were tested for their potential for the plant growth-promoting traits such as nitrogen fixation, phosphate solubilization, indole-3-acetic acid production, siderophore secretion and antifungal activity. Pot culture experiments were conducted with the screened potential endophytic cultures.Result: The 16S rRNA gene sequencing revealed that species of Enterobacter, Bacillus, Pantoea, Pseudomonas, Acromobacter, Ocrobacterium were found as endophytes in blackgram and greengram. The in vitro screening identified Bacillus pumilus (BG-E6), Pseudomonas fluorescens (BG-E5) and Bacillus licheniformis (BG-E3) from blackgram and Pseudomonas chlororaphis (GG-E2) and Bacillus thuringiensis (GG-E7) from greengram as potential plant growth-promoting endophytes. These strains showed antagonism against plant pathogenic fungi. Upon inoculation of these endophytic PGPR strains, the blackgram and greengram growth and yield got increased. Among the strains, BG-E6 recorded 14.7% increased yield in blackgram and GG-E2 accounted for a 19.5% yield increase in greengram compared to respective uninoculated control. The experimental results showed that there was a host specificity found among the endophytic bacterial cultures with pulses. The cross inoculation of endophytic strains did not perform well to enhance the growth and yield of their alternate hosts. 

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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