Microbial Diversity in Tobacco Rhizosphere Soil at Different Growth Stages

2021 ◽  
Vol 15 (5) ◽  
pp. 606-614
Author(s):  
Yanan Ruan ◽  
Shengguang Xu ◽  
Zuoxin Tang ◽  
Xiaolin Liu ◽  
Qirui Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Rhizosphere Soil ◽  
Principal Component ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Growth Stages ◽  
Soil Microbial Diversity ◽  
Different Growth Stages

Rhizosphere microorganisms are the main participants of material transformation and energy cycle in soil. To further explore its composition and variation, the tobacco rhizosphere soil were sequenced by Illumina MiSeq, the microbial community at different growth stages were analyzed and compared. The analysis of Alpha diversity showed that, the Chao1 index, Shannon index of bacteria and Chao1 index of fungi in rhizosphere soil were the highest in tobacco budding stage, while the peak of Shannon index of fungi appeared in tobacco material stage. Principal component analysis (PCA) further showed that at different growth stages, Proteobacteria was the dominant, followed by Actinobacteria, Acidobacteria and Gemmatimonadetes for bacterials; Ascomycota was the dominant, followed by Zygomycota and Basidiomycota for fungi. Under field conditions, the microbial abundance changed with the growth of tobacco, and the microbial diversity reached the peak at budding stage. The bacterial community and abundance between budding and mature stages was highly similar, while the bacterial community in vigorous growth stage is quite different. The similarity of fungal community in budding stage was very low, compared with the other stages; while in other stages was high. This study provides a theoretical basis for further understanding the relationship between tobacco rhizosphere soil microbial diversity and variation, tobacco growth and soil diseases.

scholarly journals Microbial Diversity Characteristics of Areca Palm Rhizosphere Soil at Different Growth Stages

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2706
Author(s):  
Siyuan Ma ◽  
Yubin Lin ◽  
Yongqiang Qin ◽  
Xiaoping Diao ◽  
Peng Li
Keyword(s):  
Microbial Diversity ◽  
Developmental Stages ◽  
Rhizosphere Soil ◽  
Interaction Network ◽  
Illumina Miseq ◽  
Growth Stages ◽  
Dominant Group ◽  
Soil Microbial Diversity ◽  
Bacteria And Fungi ◽  
Stage T1

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the areca palm’s developmental stages on the rhizosphere microbiota, the rhizosphere microbiota of areca palm (Areca catechu) grown in its main producing area were examined in Wanning, Hainan province, at different vegetation stages by an Illumina Miseq sequence analysis of the 16S ribosomal ribonucleic acid and internal transcribed spacer genes. Significant shifts of the taxonomic composition of the bacteria and fungi were observed in the four stages. Burkholderia-Caballeronia-Paraburkholderia were the most dominant group in stage T1 and T2; the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were decreased significantly from T1 to T2; and the genera Acidothermus and Bacillus were the most dominant in stage T3 and T4, respectively. Meanwhile, Neocosmospora, Saitozyma, Penicillium, and Trichoderma were the most dominant genera in the stage T1, T2, T3, and T4, respectively. Among the core microbiota, the dominant bacterial genera were Burkholderia-Caballeronia-Paraburkholderia and Bacillus, and the dominant fungal genera were Saitozyma and Trichoderma. In addition, we identified five bacterial genera and five fungal genera that reached significant levels during development. Finally, we constructed the OTU (top 30) interaction network of bacteria and fungi, revealed its interaction characteristics, and found that the bacterial OTUs exhibited more extensive interactions than the fungal OTUs. Understanding the rhizosphere soil microbial diversity characteristics of the areca palm could provide the basis for exploring microbial association and maintaining the areca palm’s health.

scholarly journals 83 Lifelong dynamics of the swine gut microbiome: from birth to market

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 48-48
Author(s):  
Xiaofan Wang ◽  
Tsung Cheng Tsai ◽  
Charles V Maxwell ◽  
Jiangchao Zhao
Keyword(s):  
Growth Performance ◽  
Gut Microbiome ◽  
Community Dynamics ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Growth Stages ◽  
Rrna Gene ◽  
16 S Rrna

Abstract Despite the recent advances in the swine gut microbiomes during different growth stages, a comprehensive longitudinal study of the lifelong dynamics of the swine gut microbiome is lacking. To fill this gap of knowledge, we selected seventeen piglets (PIC29*380) that were born on the same date from three sows. We collected a total of 274 rectal swabs during lactation (d 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, and 174) stages. Samples were extracted using the Powersoil DNA isolation kit (Qiagen, Hilden, Germany) and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16 S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. In general, alpha diversity including community richness (e.g., number of observed features, Chao1) and diversity (e.g., Shannon Index) showed an overall trend of increasing from lactation to the finishing stage (P < 0.01). Gradual and significant changes in community structures were also observed along the four growth stages (ANOSIM, R = 0.66; P < 0.01). Non-parametric permutational multivariate analysis of variance shows that main factors driving the lifelong community dynamics included age and diet. Seventeen phylum members were discovered in the lifelong pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant phyla. LEfSe analysis revealed 63 bacterial features that are stage specific. By using a regressing tree based Random Forest model we identified five bacterial features that are associated with swine growth performance including features 26 (Turicibacteraceae Turicibacter), 27 (Clostridium butyricum), 18 (Clostridiaceae), 19 (Clostridium perfringens) and 4 (Clostridiaceae). Characterization of the lifelong dynamics of 17 healthy pigs from birth to market provides a foundation for gut microbiome studies focusing on swine development, health and growth performance.

scholarly journals 22 Comparison of vaginal microbiome and concentrations of estradiol at artificial insemination in Brangus heifers

2020 ◽  
Vol 98 (Supplement_2) ◽  
pp. 41-42
Author(s):  
Riley D Messman ◽  
Zully Contreras-Correa ◽  
Henry A Paz ◽  
George Perry ◽  
Caleb O Lemley
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Artificial Insemination ◽  
Diversity Index ◽  
Bacterial Community Composition ◽  
Principal Component ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Vaginal Microbiome

Abstract The knowledge surrounding the bovine vaginal microbiome and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal microbiome and estradiol concentrations at time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + CIDR estrus synchronization protocol. At AI, a double guarded uterine culture swab was used to sample the anterior vaginal tract. Blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) versus nonpregnant (n = 49) on day 35. Lastly, heifers were classified into low (1.1 - 2.5 pg/ml; n = 21), medium (2.6 - 6.7 pg/ml; n = 30), and high (7.2 - 17.6 pg/ml; n = 27) concentrations of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4-V5 region from the 16S rRNA gene using the Illumina Miseq platform. ANOVA was used to compare the diversity metrics between treatment groups. PERMANOVA was utilized to determine variation in community structure. There were no statistical differences in the Shannon diversity index (alpha diversity; P = 0.336) or principal component analysis (beta diversity; P = 0.744) of pregnant versus nonpregnant animals. The vaginal microbiome of pregnant and nonpregnant animals was similar with the four most abundant phyla being Tenericutes, Proteobacteria, Fusobacteria, and Firmicutes. Overall bacterial community composition in animals with high, medium, or low concentrations of estradiol did not differ (P = 0.512). These results indicate that concentration of estradiol does not impact vaginal microbiome composition. In conclusion, the composition of the bovine vaginal microbiome, although dynamic, may not be directly linked to an animal’s reproductive ability.

scholarly journals 23 Comparison of vaginal microbiome and concentrations of estradiol at artificial insemination in Brangus heifers

2020 ◽  
Vol 98 (Supplement_2) ◽  
pp. 14-15
Author(s):  
Riley D Messman ◽  
Zully Contreras-Correa ◽  
Henry A Paz ◽  
George Perry ◽  
Caleb O Lemley
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Artificial Insemination ◽  
Diversity Index ◽  
Bacterial Community Composition ◽  
Principal Component ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Vaginal Microbiome

Abstract The knowledge surrounding the bovine vaginal microbiome and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal microbiome and estradiol concentrations at time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-day Co-Synch + CIDR estrus synchronization protocol. At AI, a double guarded uterine culture swab was used to sample the anterior vaginal tract. Blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) versus nonpregnant (n = 49) on day 35. Lastly, heifers were classified into low (1.1 - 2.5 pg/ml; n = 21), medium (2.6 - 6.7 pg/ml; n = 30), and high (7.2 - 17.6 pg/ml; n = 27) concentrations of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4-V5 region from the 16S rRNA gene using the Illumina Miseq platform. ANOVA was used to compare the diversity metrics between treatment groups. PERMANOVA was utilized to determine variation in community structure. There were no statistical differences in the Shannon diversity index (alpha diversity; P = 0.336) or principal component analysis (beta diversity; P = 0.744) of pregnant versus nonpregnant animals. The vaginal microbiome of pregnant and nonpregnant animals was similar with the four most abundant phyla being Tenericutes, Proteobacteria, Fusobacteria, and Firmicutes. Overall bacterial community composition in animals with high, medium, or low concentrations of estradiol did not differ (P = 0.512). These results indicate that concentration of estradiol does not impact vaginal microbiome composition. In conclusion, the composition of the bovine vaginal microbiome, although dynamic, may not be directly linked to an animal’s reproductive ability.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P &lt; .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals Different Cultivation Environments Affect the Yield, Bacterial Community and Metabolites of Cordyceps cicadae

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhaoying Zeng ◽  
Dan Mou ◽  
Li Luo ◽  
Wenlin Zhong ◽  
Lin Duan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Natural Habitat ◽  
Bacterial Community Composition ◽  
Pinus Massoniana ◽  
Growth Stages ◽  
Natural Habitats ◽  
Entomogenous Fungus ◽  
Cordyceps Cicadae ◽  
Glass Bottles ◽  
Different Growth Stages

Cordyceps cicadae is an entomogenous fungus with important uses in traditional Chinese medicine. However, its wild resources have not met consumers’ demand due to excessive harvesting practices. Artificial cultivation is therefore an important alternative, but research on cultivating C. cicadae in natural habitats has not been reported. In this study, we aimed to explore the viability of cultivating C. cicadae in a natural habitat, in the soil of Pinus massoniana forest. We assessed and compared the yield, metabolite contents and bacterial community composition of C. cicadae grown in the Antheraea pernyi pupae at different growth stages, and under different cultivation conditions, in the soil of a natural habitat and in sterile glass bottles. Our results showed that cultivating C. cicadae in a natural habitat is feasible, with up to 95% of pupae producing C. cicadae fruiting bodies. The content of nitrogen compounds (amino acids) in C. cicadae cultivated in a natural habitat was significantly higher than in glass bottles, while the yield and carbon compound (mannitol and polysaccharide) and nucleoside (cordycepin and adenosine) contents were lower. Different bacterial genera were enriched in C. cicadae at different growth stages and cultivation environments, and these bacterial genera were closely related to metabolites contents during growth. This study demonstrated the viability of a novel cultivation method of C. cicadae, which could be used as an alternative to wild stocks of this fungus. These findings provided new insights into the growth mechanism of C. cicadae and its interaction with soil microorganisms.

scholarly journals 408 Effect of monensin intake during a stocker phase and subsequent finishing phase on rumen bacterial diversity of beef steers

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 163-164
Author(s):  
Caleb P Weiss ◽  
Paul A Beck ◽  
John T Richeson ◽  
Dexter J Tomczak ◽  
Jianmin Chai ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pennisetum Glaucum ◽  
Rumen Fluid ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Beef Steers ◽  
Diet Change ◽  
Gluten Feed

Abstract Three monensin levels during a stocker phase (0, 800, 1600 g/ton fed in a free choice mineral) and two levels during finishing [0 (U) or 37.5 mg/kg diet DM (M)] were used to determine the effects of monensin supplementation during a stocker and subsequent finishing phase on rumen bacterial communities of beef steers. Thirty calves were fed pearl millet (Pennisetum glaucum) hay with soybean hull and corn gluten feed supplement (0.5% BW daily, AF basis) or grazed fall wheat pasture (Triticum aestivum) during a stocker phase and then transported 1,067 km to Canyon, TX, for finishing. Rumen fluid was collected on d 0, 28, and the end of the stocker phase (d 85). Samples were also obtained at feedlot d 0, 14, 28, 56, and immediately prior to a diet change to include a beta-adrenergic agonist and before shipping for harvest. Rumen microbiota were characterized by next generation sequencing the 16S v4 hypervariable region with the Illumina MiSeq platform. During the stocker phase, Prevotella and Bacteroidetes were the most dominant genus regardless of diet or treatment. Monensin decreased (P ≤ 0.01) alpha diversity (Shannon Index) for cattle consuming hay on d 28 of the stocker phase. In the feedlot, Prevotella, Lachnospiraceae, and Bacteroidetes were the most abundant genus. Steers that were previously on the 0 and 1600 treatments during the stocker phase and were fed monensin at the feedlot had decreased alpha diversity (P = 0.04) on feedlot d 14 compared to those that did not. Monensin at the feedlot tended to increase alpha diversity on d 28 for cattle previously on the 1600 treatment (P = 0.06), and on d 56 for cattle previously on the 0 treatment (P = 0.06). This experiment provides a better understanding of the effect of monensin on rumen bacterial communities throughout production.

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter

2018 ◽  
Vol 81 (9) ◽  
pp. 1557-1564
Author(s):  
LINLIN JIANG ◽  
JIANLONG ZHANG ◽  
JINXIU TANG ◽  
MENG LI ◽  
XIAOYU ZHAO ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Total Concentration ◽  
Growth Period ◽  
Growth Cycle ◽  
Growth Stages ◽  
Community Structures ◽  
Dynamic Pattern ◽  
Different Growth Stages

ABSTRACT The aim of the present study was to analyze the aerosol concentrations and microbial community structures in closed cage broiler houses at different broiler growth stages to assess the dynamic pattern of microbial aerosols in closed cage systems. Our results revealed that the total concentration of bacterial aerosols gradually increased during the growth cycle of broilers. High-throughput sequencing of 16S rDNA revealed that microbial compositions differed tremendously during different growth stages, although Firmicutes and Proteobacteria were the dominant taxa in samples from all broiler growth stages. At the genus level, dominant phylotypes displayed great variation during different growth stages. Escherichia and Shigella were the most dominant taxa throughout the growth cycle, increasing from 4.3 to 12.4% as the broilers grew. The alpha index revealed that the microbial diversity displayed significant differences between the different growth stages and that the bacterial community had the highest diversity when broilers were 22 days old. High-throughput sequencing analyses revealed that environmental microbes and opportunistic pathogens had relatively high abundances during the winter growth period. The data revealed the composition and aerodynamic diameters of microbial aerosols in closed cage broiler houses at different broiler growth stages in winter. The results also enabled us to elucidate the dynamic pattern of microbial aerosols in broiler houses in response to bacterial communities. Our results may provide a basis for developing technologies for air quality control in caged poultry houses.

scholarly journals Early life home microbiome and hyperactivity/inattention in school-age children

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lidia Casas ◽  
Anne M. Karvonen ◽  
Pirkka V. Kirjavainen ◽  
Martin Täubel ◽  
Heidi Hyytiäinen ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Early Life ◽  
Fungal Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
School Age Children ◽  
Sequencing Data ◽  
Logistic Regression Models ◽  
Diversity Measures ◽  
Early Life Exposure

AbstractThis study evaluates the association between indoor microbial diversity early in life and hyperactivity/inattention symptoms in children at ages 10 and 15 years.A random sample enriched with subjects with hyperactivity/inattention at age 15 years was selected from the German LISA birth cohort. Bedroom floor dust was collected at age 3 months and 4 bacterial and fungal diversity measures [number of observed operational taxonomic units (OTUs), Chao1, Shannon and Simpson indices] were calculated from Illumina MiSeq sequencing data. Hyperactivity/inattention was based on the Strengths and Difficulties Questionnaire at ages 10 and 15 (cut-off ≥7). Adjusted associations between 4 diversity measures in tertiles and hyperactivity/inattention were investigated with weighted and survey logistic regression models. We included 226 individuals with information on microbial diversity and hyperactivity/inattention. Early life bacterial diversity was inversely associated with hyperactivity/inattention at age 10 [bacterial OTUs (medium vs low: aOR = 0.4, 95%CI = (0.2–0.8)) and Chao1 (medium vs low: 0.3 (0.1–0.5); high vs low: 0.3 (0.2–0.6)], whereas fungal diversity was directly associated [Chao1 (high vs low: 2.1 (1.1–4.0)), Shannon (medium vs low: 2.8 (1.3–5.8)), and Simpson (medium vs low: 4.7 (2.4–9.3))]. At age 15, only Shannon index was significantly associated with hyperactivity/inattention [bacteria (medium vs low: 2.3 (1.2–4.2); fungi (high vs low: 0.5 (0.3–0.9))]. In conclusion, early life exposure to microbial diversity may play a role in the psychobehavioural development. We observe heterogeneity in the direction of the associations encouraging further longitudinal studies to deepen our understanding of the characteristics of the microbial community underlying the observed associations.

Sign in / Sign up

Export Citation Format

Share Document