scholarly journals Genetic Control of Rhizosphere Microbiome of Cotton Plant Under Field Conditions

2021 ◽  
Author(s):  
Feng Wei ◽  
Zili Feng ◽  
Chuanzhen Yang ◽  
Lihong Zhao ◽  
Yalin Zhang ◽  
...  
Keyword(s):  
Genetic Control ◽  
Cotton Plant ◽  
Principal Components ◽  
Alpha Diversity ◽  
Differential Resistance ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Rhizosphere Microbiome ◽  
Random Variability

Abstract Background: Understanding the extent of heritability of plant-associated microbiome (phytobiome) is critical for exploitation of phytobiome in agriculture. Two crosses were made between pairs of cotton cultivars with differential resistance to the Verticillium wilt. F2 plants were grown together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities.Results: F2 hybrid offspring of both crosses had higher alpha diversity indices as well as greater variability than the two parents. Two types of data were used generated to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial OTUs. For the L1×Z49 cross, the variance among the 100 progeny genotypes (VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2×J11 cross, the corresponding values were 10 and 20 PCs. Out of the top 100 OTUs, 29 fungal OTUs and 10 bacterial OTUs had VT that was significantly greater than VE for the L1×Z49 cross; the corresponding value for the Z2×J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%.Conclusions: These results suggested the existence of genetic control in terms of rhizosphere microbiome in cotton.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Investigation of Age-Related Changes in the Skin Microbiota of Korean Women

2020 ◽  
Vol 8 (10) ◽  
pp. 1581
Author(s):  
Minseok Kim ◽  
Tansol Park ◽  
Jung Im Yun ◽  
Hye Won Lim ◽  
Na Rae Han ◽  
...  
Keyword(s):  
Age Groups ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Korean Women ◽  
Skin Microbiota ◽  
Microbial Distribution ◽  
Age Related ◽  
Age Related Changes

The microbiota of human skin is influenced by host and environmental factors. To determine if chronological age influences the composition of the skin microbiota on the forehead and hands, 73 Korean women were sorted into one of three age groups: (1) 10–29 years (n = 24), (2) 30–49 years (n = 21), and (3) 50–79 years (n = 28). From the 73 women, 146 skin samples (two skin sites per person) were collected. 16S rRNA gene amplicon sequencing was then conducted to analyze the skin microbiota. The overall microbial distribution varied on the forehead but was similar on the hands across the three age groups. In addition, the composition of the skin microbiota differed between the forehead and hands. Commensal microbiota, such as Streptococcus, Staphylococcus, Cutibacterium, and Corynebacterium, which contribute to maintaining skin health via dominant occupation, were affected by increasing age on forehead and hand skin. Alpha diversity indices increased significantly with age on forehead skin. This study indicates that older people may be more susceptible to pathogenic invasions due to an imbalanced skin microbiota resulting from age-related changes. The results of our study may help develop new strategies to rebalance skin microbiota shifted during aging.

scholarly journals The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingjing Chang ◽  
Yu Sun ◽  
Lei Tian ◽  
Li Ji ◽  
Shasha Luo ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Wild Rice ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogen Invasion ◽  
Rice Rhizosphere ◽  
Soilborne Fungi

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.

scholarly journals Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 244 ◽  
Author(s):  
Mohammad Murtaza Alami ◽  
Jinqi Xue ◽  
Yutao Ma ◽  
Dengyan Zhu ◽  
Aqleem Abbas ◽  
...  
Keyword(s):  
Cropping Systems ◽  
Cropping System ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Soil Samples ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Coptis Chinensis ◽  
The Sustainable Development ◽  
Fungal Community Structure

Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. Coptis chinensis Franch is one of the most important medicinal plants in China. In the current study, we provide detailed information regarding the diversity and composition of rhizospheric fungal communities of the C. chinensis plants in continuous cropping fields and fallow fields in two seasons (winter and summer), using next-generation sequencing. Alpha diversity was higher in the five-year C. chinensis field and lower in fallow fields. Significant differences analysis confirmed more fungi in the cultivated field soil than in fallow fields. Additionally, PCoA of beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Five fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycota) were identified from the soil samples in addition to the unclassified fungal taxa and Cryptomycota, and among these phyla, Ascomycota was predominantly found. FUNGuild fungal functional prediction revealed that saprotroph was the dominant trophic type in all two time-series soil samples. Redundancy analysis (RDA) of the dominant phyla data and soil physiochemical properties revealed the variations in fungal community structure in the soil samples. Knowledge from the present study could provide a valuable reference for solving the continuous cropping problems and promote the sustainable development of the C. chinensis industry.

scholarly journals Different Responses of Soil Bacterial and Fungal Communities to 3 Years of Biochar Amendment in an Alkaline Soybean Soil

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenhui Gao ◽  
Ke Gao ◽  
Zonghao Guo ◽  
Yuan Liu ◽  
Li Jiang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Chemical Fertilizer ◽  
Fungal Communities ◽  
Agricultural Ecosystem ◽  
Bacterial Phyla ◽  
Rhizosphere Soils ◽  
Biochar Amendment

Biochar as a soil amendment has been regarded as a promising way to improve soil fertility. However, the response of microbial community after biochar and biochar compound fertilizer (BCF) application has not been thoroughly elucidated. This study evaluated the changes in abundance and composition of bacterial and fungal communities using quantitative real-time PCR (qPCR) and Illumina MiSeq amplicon sequencing. The field experiment ran for 3 years and comprised five treatments: chemical fertilizer as control (CK), straw-returning combined with chemical fertilizer (CS), low biochar application combined with chemical fertilizer (LB), high biochar application combined with chemical fertilizer (HB) and BCF. The results showed that biochar amendment results no changes in the abundance and diversity of bacteria in the bulk and rhizosphere soils. However, the abundance of soil fungi was significantly increased by biochar amendment (LB and HB). LB treatment significantly increased the fungal alpha diversity, while there was no significant change under HB. Furthermore, the dominant bacterial phyla found in the samples were Proteobacteria, Actinobacteria, and Acidobacteria. Biochar addition increased the relative abundance of Actinobacteria in both bulk and rhizosphere soils. The dominant fungal phyla were Ascomycota, Mortierellomycota, and Basidiomycota. The relative abundance of Ascomycota significantly decreased, but Mortierellomycota significantly increased in LB and HB. In addition, redundancy analysis indicated that the changes in bacterial and fungal communities are associated with soil properties such as SOC and TN, which are crucial contributors in regulating the community composition. This study is expected to provide significant theoretical and practical knowledge for the application of biochar in agricultural ecosystem.

scholarly journals Diet Induces the Difference of Gut Fungal Communities between Anser erythropus Wintering at Shengjin and Caizi Lakes, China

2021 ◽  
Author(s):  
Gang Liu ◽  
Zhizhong Gong ◽  
Jiahui Feng ◽  
Na Xu
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogenic Species ◽  
Potential Pathogen ◽  
Host Nutrition ◽  
The Difference ◽  
Serious Disease ◽  
Anser Erythropus

Abstract The gut microbiota play major roles in host nutrition and metabolism, and even potential to cause serious disease for animals and human, however, the knowledge of waterbirds’ gut fungal communities are quite limited at present. In this paper, the gut fungal communities and infer the potential pathogens isolated from the feces of Anser erythropus wintering at Shengjin Lake (SJ) and Caizi Lake (CZ) were investigated based on ITS gene region by using high-throughput sequencing. 1,302,562 valid tags corresponding to 2,102 OTUs were retained from 20 fecal samples, including 10 samples per lake. The OTUs from SJ geese represented seven phyla and 27 classes, seven phyla and 28 classes were identified from CZ samples. Ascomycota, Basidiomycota, Zygomycota and Rozellomycota were the dominant gut fungal phyla in this study, accounted for 61.60%, 35.60%, 1.84%, and 0.30% of the OTUs, respectively. The alpha diversity indices showed significantly different between the geese from SJ and CZ. The Anser erythropus mainly ate Poaceae spp. at SJ, while Carex spp. component was identified at CZ, suggesting that the variations in fungal community between the two lake geese might be induced by different diets. We also observed a fungal pattern with a higher number of significant correlations to bacterial genus, and Ceratobasidium, Tomentella, Paurocotylis, Tuber, Podospora and Mortierella were core fungal genus in the two lake geese. Nine potential pathogenic species were identified in the guts across all samples of Anser erythropus at SJ and CZ, it also showed the relative abundance of potential pathogen was significantly higher from SJ samples than that from CZ samples. These findings expanded our knowledge on the gut fungi for waterbirds, indicating the fungi are highly sensitive to diet at two lakes and should pay more attention to the potential pathogenic species of Anser erythropus.

scholarly journals Streptomyces Application Triggers Reassembly and Optimization of the Rhizosphere Microbiome of Cucumber

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 413
Author(s):  
Yanjiang Zhang ◽  
Tian Zhang ◽  
Zhijing Xue ◽  
Yifan Liu ◽  
Yongzhe Li ◽  
...  
Keyword(s):  
Plant Growth ◽  
Relative Abundance ◽  
Stress Resistance ◽  
Growth Promotion ◽  
Alpha Diversity ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Cucumis Sativus L ◽  
Genus Streptomyces ◽  
Rhizosphere Microbiome

Streptomyces partum Act12 and Streptomyces roche D74 are biocontrol strains that can promote plant growth and enhance stress resistance in different crops. However, their effects on the rhizosphere microbiome and the role of the reassembled microbiome in plant growth promotion and stress resistance enhancement remain unclear. This study investigated the variation in the rhizosphere microbiome induced by Streptomyces application through a cucumber (Cucumis sativus L. cv. “Youliang”) pot experiment. The bacterial and fungal communities of rhizosphere soils inoculated with and without Streptomyces were, respectively, compared based on 16S rRNA and internal transcribed spacer rRNA gene sequences. Following Streptomyces application, the bacterial alpha diversity increased significantly, while the fungal alpha diversity exhibited the opposite trend. The bacterial and fungal communities’ compositions clearly shifted in the inoculated soil. Compared with the uninoculated control, the relative abundance of the genus Streptomyces increased by 68.3%, and the bacterial co-occurrence network in the rhizosphere soil was enriched significantly. The relative abundance of bacteria associated with nitrogen fixation was increased by 7.5% following Streptomyces application. Based on the results of this study, we conclude that the application of Streptomyces Act12 and D74 can be used to reassemble and optimize the rhizosphere microbiome of cucumber, which is conducive to plant survival.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2414
Author(s):  
Laura Sanjulián ◽  
Alexandre Lamas ◽  
Rocío Barreiro ◽  
Alberto Cepeda ◽  
Cristina A. Fente ◽  
...  
Keyword(s):  
Breast Milk ◽  
16S Rrna ◽  
Human Milk ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Maternal Body Mass Index ◽  
16S Rrna Amplicon Sequencing ◽  
Spanish Women ◽  
Calcium Magnesium ◽  
Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

scholarly journals Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components

2021 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
Zahra A. Barandouzi ◽  
Joochul Lee ◽  
Kendra Maas ◽  
Angela R. Starkweather ◽  
Xiaomei S. Cong
Keyword(s):  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Cross Sectional Study ◽  
Caffeine Intake ◽  
Caffeine Consumption ◽  
Cross Sectional ◽  
Food Components ◽  
Irritable Bowel

The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.

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