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

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.

Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

2021 ◽  
Author(s):  
Yanbo Liu ◽  
Mengxiao Sun ◽  
Pei Hou ◽  
Wenya Wang ◽  
Xiangkun Shen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Qualitative Analysis ◽  
Volatile Compounds ◽  
High Throughput ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Solid Phase ◽  
Gas Chromatography Mass Spectrometry ◽  
Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

scholarly journals Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

2020 ◽  
Author(s):  
Chuanbo Zhang ◽  
Chao-Hui Ren ◽  
Yan-Li Wang ◽  
Qi-Qi Wang ◽  
Yun-Sheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Bioactive Metabolites ◽  
Fungal Community Structure ◽  
Ophiocordyceps Sinensis ◽  
Culturable Fungi ◽  
Culture Dependent

Abstract Background The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approach. Results A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices (EMC), Ophiocordyceps, Sebacinia, Archaeorhizomyces were predominant genera with the abundance of 95.86%, 1.14%, 0.85%, respectively. Total 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, Unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, Unclassified Ascomycota, Unclassified Fungi were predominant genera with an average abundance of 53.32%, 8.69%, 8.12%, 8.12%, 7.21%, 4.6%, 3.08% and 3.05%, respectively. The fungal communities in external mycelial cortices (EMC) were significantly distinct from the soil microhabitat (Soil). Meanwhile, seven culture media that benefit for the growth of O. sinensis were used to isolate culturable fungi at 16 °C, resulted in 77 fungal strains isolated for rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora, Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera of total isolates. Conclusions The significantly distinction and overlap in fungal community structure between two approaches highlight that integration of approaches would generate more information than either of them. Our finding is the first investigation of fungal community structure of natural O. sinensis by two approachs, provide new insight into O. sinensis associated fungi, and support that microbiota of O. sinensis is an untapped source for novel bioactive metabolites discovery.

scholarly journals Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest

2016 ◽  
Vol 82 (9) ◽  
pp. 2632-2643 ◽  
Author(s):  
Hui Sun ◽  
Eeva Terhonen ◽  
Andriy Kovalchuk ◽  
Hanna Tuovila ◽  
Hongxin Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
High Throughput ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Soil Layer ◽  
Fungal Community Composition ◽  
Content Type ◽  
Boreal Peatlands

ABSTRACTBoreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P< 0.001) and tree species (P< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P< 0.04). The availability of soil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera ofAgaricomycotinaidentified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

The Impact of Reclaimed Water Irrigation on Soil Microbial Community Structure

2014 ◽  
Vol 955-959 ◽  
pp. 3635-3639 ◽  
Author(s):  
Ji Hua Wang ◽  
Xue Gong ◽  
Jian Fei Guan ◽  
Hui Yan Xing
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Soil Column ◽  
Reclaimed Water ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact ◽  
Reclaimed Water Irrigation

The reclaimed water treated in a Harbin recycled water plant has been taken as a target of research, by using microbial traditional culture method and tablet coated counting method, discussing the influence of the reclaimed water irrigation on soil microbial community structure through the method of short-term indoor simulated soil column irrigation. The results shows that the reclaimed water irrigation can significantly increase the quantity of bacteria and actinomycetes in the surface 0-20 cm layer soil, but it has little affect on 20-40 cm and 40-60 cm layer soil. Microbial community structure and diversity were changed relatively with the irrigation of reclaimed water, which embodied the increase or decrease of dominant and subdominant groups, the disappearance of non-dominant groups sensitive to reclaimed water, the appear or disappear of the other part of the occasional groups.

scholarly journals High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 633 ◽  
Author(s):  
Maria Paola Pisano ◽  
Nicole Grandi ◽  
Enzo Tramontano
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Large Fraction ◽  
Expression Patterns ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Retroviral Infections ◽  
The Impact

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

scholarly journals High‐throughput sequencing reveals the core gut microbiome of Bar‐headed goose ( Anser indicus ) in different wintering areas in Tibet

2016 ◽  
Vol 5 (2) ◽  
pp. 287-295 ◽  
Author(s):  
Wen Wang ◽  
Jian Cao ◽  
Fang Yang ◽  
Xuelian Wang ◽  
Sisi Zheng ◽  
...  
Keyword(s):  
High Throughput ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
The Core ◽  
Wintering Areas ◽  
Anser Indicus
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