scholarly journals Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongshuo Xu ◽  
Wenli Jiang ◽  
Dandan Qin ◽  
Taiguo Liu ◽  
Jianmin Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Microbial Composition ◽  
Wheat Varieties ◽  
Resistant Varieties ◽  
Abundance And Diversity ◽  
Dwarf Bunt ◽  
Wheat Tissues

AbstractDwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

scholarly journals Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingwu Shi ◽  
Hongmei Yang ◽  
Ming Chu ◽  
Xinxiang Niu ◽  
Ning Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Growth Period ◽  
Tianshan Mountains ◽  
Rhizosphere Bacteria ◽  
Microbial Composition ◽  
Ecological Regions ◽  
Rhizosphere Fungi ◽  
Dominant Bacteria ◽  
North And South

The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.

scholarly journals SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification

2017 ◽  
Author(s):  
Manuel Tardaguila ◽  
Lorena de la Fuente ◽  
Cristina Marti ◽  
Cécile Pereira ◽  
Francisco Jose Pardo-Palacios ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Full Length ◽  
The Novel ◽  
Extensive Evaluation ◽  
Long Reads ◽  
Long Read ◽  
Novel Transcripts ◽  
Mouse Transcriptome

ABSTRACTHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

scholarly journals Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

2019 ◽  
Vol 68 (2) ◽  
pp. 281-284
Author(s):  
LIN WANG ◽  
ZHIYING LI ◽  
RUIRUI LIU ◽  
LULU LI ◽  
WEIWEI WANG
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Rhizosphere Soil ◽  
Structural Diversity ◽  
Crop Productivity ◽  
Mature Stage ◽  
Growth Stages ◽  
Abundance And Diversity ◽  
Two Stages ◽  
Dominant Bacteria

Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.

scholarly journals Analysis of Sour Porridge Microbiota and Improvement of Cooking Quality via Pure Culture Fermentation Using Lacticaseibacillus paracasei Strain SZ02

2021 ◽  
Vol 12 ◽  
Author(s):  
Cheng Wang ◽  
Yunhe Xu ◽  
Bin Yu ◽  
Aibo Xiao ◽  
Yuhong Su ◽  
...  
Keyword(s):  
High Throughput ◽  
Pure Culture ◽  
Fermentation Process ◽  
High Throughput Sequencing ◽  
Cooking Quality ◽  
Microbial Composition ◽  
Natural Fermentation ◽  
Acid Producing Bacteria ◽  
Dominant Bacteria

The microbial composition of sour porridge at different fermentation times was analyzed through high-throughput sequencing, and a pure culture fermentation process was established to optimize production process and improve the edible quality of the porridge. In natural fermentation, Firmicutes and Proteobacteria were abundant throughout the process. Specifically, Aeromonas, Acinetobacter, and Klebsiella were dominant on fermentation days 1–5 (groups NF-1, NF-3, and NF-5), while Lactobacillus and Acetobacter gradually became the dominant bacteria on fermentation day 7 (group NF-7). Further, we isolated one strain of acid-producing bacteria from sour porridge, identified as Lacticaseibacillus paracasei by 16SrRNA sequencing and annotated as strain SZ02. Pure culture fermentation using this strain significantly increased the relative starch and amylose contents of the porridge, while decreasing the lipid, protein, and ash contents (P < 0.05). These findings suggest that sour porridge produced using strain SZ02 has superior edible qualities and this strategy may be exploited for its industrial production.

scholarly journals Comparative analysis of rhizosphere soil physiochemical characteristics and microbial communities between rusty and healthy ginseng root

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xingbo Bian ◽  
Shengyuan Xiao ◽  
Yan Zhao ◽  
Yonghua Xu ◽  
He Yang ◽  
...  
Keyword(s):  
Community Structure ◽  
Rhizosphere Soil ◽  
Chemical Properties ◽  
Ginseng Root ◽  
Available Phosphorus ◽  
Abundance And Diversity ◽  
Physical And Chemical ◽  
The Relationship ◽  
Soil Changes

Abstract Ginseng rusty root (GRR) symptom is one of the primary diseases of ginseng. There has been a problem of ginseng rusty root, leading to a severe decline in the quality of ginseng. To clarify the relationship between root symptoms of ginseng rust and soil, the physical and chemical properties, enzyme activity, community structure and microbial diversity of GRR and healthy ginseng (HG) rhizosphere soil were analyzed and compared. The pH and redox potential (Eh) of GRR soil decreased, and the contents of total phosphorus (TP), available phosphorus (AP), and available potassium (AK) decreased. The activity of catalase and phosphatase and invertase was lower than that of HG groups. Besides, the microbial community of GRR rhizosphere soil changes much, and its abundance and diversity are significantly reduced. The community structure of GRR rhizosphere soil also shows apparent differences, and the samples of the HG group gathered together, and the samples of the GRR group were dispersed. In general, GRR was closely associated with decreases in soil pH and Eh; decreases in TP, AP, and AK; decreases in the activity of several enzymes. Additionally, it is strongly associated with an increase in pathogenic microorganisms such as Ilyonectria and a reduction of beneficial microorganisms such as Tremellomycetes Acidobacteria subgroup 6 and Gemmatimonadetes.

scholarly journals Identification of Triticum aestivum L., Triticum spelta L. and Triticum durum DESF. genotypes on the HMW-GS base

2010 ◽  
Vol 56 (No. 2) ◽  
pp. 82-86
Author(s):  
V. Oslovičová ◽  
Z. Gálová ◽  
M. Chňapek ◽  
Ž. Balážová
Keyword(s):  
Triticum Aestivum ◽  
Triticum Durum ◽  
Reference Method ◽  
Bread Making ◽  
Triticum Spelta ◽  
Wheat Varieties ◽  
Sds Page ◽  
Technological Quality

The main goal of this work was to identify genotypes of three wheat species Triticum aestivum</i> L., <i>Triticum spelta</i> L., <i>Triticum durum</i> DESF.) on the basis of individual high-molecular-weight glutenin subunits (HMW-GS) and to predict their technological quality. Detection of HMW-GS was carried out by the standard reference method ISTA SDS-PAGE and the Glu-score was calculated according to the catalogue of alleles for HMW-GS. Among the common wheat varieties the highest Glu-score (10) was determined for the cultivars Axis, Istra and Solara. The most frequently occurring HMW-GS in genotypes of <i>Triticum aestivum</i> L. were 0; 7 + 9; 5 + 10. On the other hand, in the spelt wheat the highest frequency of HMW-GS was detected for 2*; 6 + 8; 2 + 12. The Glu-score for <i>Triticum spelta</i> L. genotypes ranged from 6 to 8. Among the <i>Triticum durum</i> DESF. cultivars, up to 71% were characterized by Glu-score 4, which predetermines them for special baking purposes. The most frequent combination of HMW-GS in durum wheat was 0 and 7 + 8. Thus, SDS PAGE of HMW-GS can be used for identification, differentiation and characterization of different species of wheat and for prediction of bread-making quality of wheat.

scholarly journals Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

2020 ◽  
Vol 8 (1) ◽  
pp. 134 ◽  
Author(s):  
Rodrigo García-López ◽  
Fernanda Cornejo-Granados ◽  
Alonso A. Lopez-Zavala ◽  
Filiberto Sánchez-López ◽  
Andrés Cota-Huízar ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Low Cost ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Hypervariable Regions ◽  
Reference Databases ◽  
Marine Product ◽  
V3 Region

The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.

scholarly journals Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

2018 ◽  
Author(s):  
Lingying Dai ◽  
Limei Wang ◽  
Jiang Sun ◽  
Lixue Zheng ◽  
Bin Qi
Keyword(s):  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Bacterial Populations ◽  
Three Stages ◽  
Dominant Bacteria ◽  
The Relationship ◽  
Insight Into

AbstractHigh-throughput sequencing was used to reveal the highly diverse bacterial populations in shrimp paste at different fermentation stages. We studied three stages of fermentation and obtained 448,916 reads. Using this approach, we revealed the presence of 30 phyla, 55 classes, 86 orders, 206 families and 695 genera of bacteria in the shrimp paste. Shrimp paste in fermentation metaphase had a more diverse microbiota than that in fermentation prophase and fermentation anaphase. Diversity appeared greatest in fermentation anaphase. The four dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The most common genera were Psychrobacter, Halomonas, Bacillus, Alteribacillus, and Lactococcus. Their content varied at different stages of fermentation. All the microbiome presented a variety of changes in the microbial diversity of shrimp paste.ImportanceMost research on the microbial diversity of shrimp paste has focused on the shrimp culture environment, or the chemical composition and sensory attributes of the paste. Little research has been conducted on the microbial diversity and composition of shrimp paste. The relationship between microbes and the flavor and quality of shrimp paste has thus been unknown. We therefore analyzed the microbial composition and variation of shrimp paste at different stages of fermentation. The dominant bacteria in fermentation prophase, metaphase, and anaphase were identified. Our preliminary findings give some insight into which microbes contribute to the flavor of shrimp paste and suggest how to improve its flavor. In addition, our findings are relevant to optimizing the production of shrimp paste and guaranteeing its quality and safety.

scholarly journals Abundance and diversity of resistomes differ between healthy human oral cavities and gut

2019 ◽  
Author(s):  
Victoria R. Carr ◽  
Elizabeth Witherden ◽  
Sunjae Lee ◽  
Saeed Shoaie ◽  
Peter Mullany ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Oral Cavity ◽  
Resistance Genes ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Microbial Composition ◽  
Healthy Human ◽  
Antimicrobial Resistance Genes ◽  
Stool Samples ◽  
Abundance And Diversity

AbstractThe global threat of the “antimicrobial resistance apocalypse” that has arisen in recent years has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the “resistome”, in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes, and little is known about their abundance and diversity, or how their profile compares with antimicrobial resistance genes in the gut. Here we analyse the resistome profiles of 788 oral cavities worldwide and compare these profiles with paired stool samples from shotgun metagenomic data. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. However, the abundance of these antimicrobial resistance classes do not correlate with antibiotic prescription rates. A greater similarity was found in interpersonal resistomes between the same body sites than intrapersonal resistomes across different body sites. Between individuals, the oral cavity contains the highest and lowest abundances of specific antimicrobial resistance genes, but a lower diversity of resistance genes compared to the gut, which is likely influenced by differences in microbial composition and exposure to antimicrobial selection pressures. Co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. This is the first study to date that characterises the oral cavity resistome worldwide, identifying its distinctive signatures compared to the gut.Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body.

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