scholarly journals Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

2019 ◽  
Author(s):  
Federica Caradonia ◽  
Domenico Ronga ◽  
Marcello Catellani ◽  
Cleber Vinícius Giaretta Azevedo ◽  
Rodrigo Alegria Terrazas ◽  
...  
Keyword(s):  
Crop Production ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Two Component System ◽  
Tomato Root ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing ◽  
Soil Interface

ABSTRACTThe microbial communities thriving at the root-soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilisers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilisers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root-soil interface is modulated by and in responses to the type of nitrogen fertiliser applied to the field.

scholarly journals Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

2019 ◽  
Vol 3 (4) ◽  
pp. 315-325 ◽  
Author(s):  
Federica Caradonia ◽  
Domenico Ronga ◽  
Marcello Catellani ◽  
Cleber Vinícius Giaretta Azevedo ◽  
Rodrigo Alegria Terrazas ◽  
...  
Keyword(s):  
Crop Production ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
16S Rrna Gene Sequencing ◽  
Nitrogen Fertilizers ◽  
Rrna Gene ◽  
Tomato Root ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing ◽  
Soil Interface

The microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root−soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 638
Author(s):  
Caitlin E. Older ◽  
Aline Rodrigues Hoffmann ◽  
Kathleen Hoover ◽  
Frane Banovic
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
16S Rrna Gene Sequencing ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Bacterial Microbiota ◽  
Starting Point ◽  
Rrna Gene Sequencing ◽  
Antimicrobial Treatments ◽  
Staphylococcus Spp

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

scholarly journals Assessment of Oral Vancomycin-Induced Alterations in Gut Bacterial Microbiota and Metabolome of Healthy Men

2021 ◽  
Vol 11 ◽  
Author(s):  
Andrew HyoungJin Kim ◽  
Yujin Lee ◽  
Eunwoo Kim ◽  
Sang Chun Ji ◽  
Jae-Yong Chung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Vancomycin ◽  
Healthy Men ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing ◽  
Metabolomics Analysis

Several classes of antibiotics have reduced the mortality caused by infectious diseases; however, orally administered antibiotics alter the composition of gut microbiota, leading to dysbiosis-related disease. Therefore, in this study, we used 16S rRNA gene sequencing- and metabolomics-based approaches to investigate the effects of oral vancomycin on gut bacterial microbiota and the metabolome in biospecimens collected from healthy men. Samples collected from 11 healthy men were analyzed using 16S rRNA gene sequencing and metabolomics. 16S rRNA gene sequencing was performed to analyze the gut bacterial microbiota, and GC-TOFMS-based untargeted metabolomics was performed to analyze fecal, urine, and plasma metabolomics. Spearman’s rank correlation was utilized to explore the associations between gut bacterial microbiota and metabolome. Fecal 16S rRNA gene sequencing analysis showed decreased relative abundance of genera belonging to the phyla Bacteroidetes and Firmicutes, and increased relative abundance of genera of the phyla Proteobacteria and Fusobacteria. Fecal metabolomics analysis showed that levels of uracil, L-aspartic acid, lithocholic acid, and deoxycholic acid were significantly higher at baseline, whereas that of dihydrouracil was significantly higher after vancomycin administration. No significant metabolic markers were selected from urine and plasma metabolomics analysis. This study demonstrates that oral vancomycin administration induces alterations in gut bacterial microbiota and metabolome. Correlation analysis between our two datasets shows that alteration of the gut bacterial microbiota, induced by oral vancomycin, potentially affected the systemic activity of dihydropyrimidine dehydrogenase. This correlation should be further examined in future studies to define the effects of gut bacterial microbiota on drug-metabolizing enzymes, thereby contributing to the development of personalized therapy.

scholarly journals Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

Animals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 31
Author(s):  
Elisa Cotozzolo ◽  
Paola Cremonesi ◽  
Giulio Curone ◽  
Laura Menchetti ◽  
Federica Riva ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Large Intestine ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Productive Performance ◽  
Bacterial Populations ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing

The microbiota is extremely important for the animal’s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

scholarly journals Insights into the Oral Bacterial Microbiota of Sows

2021 ◽  
Vol 9 (11) ◽  
pp. 2314
Author(s):  
Jasmine Hattab ◽  
Giuseppe Marruchella ◽  
Alberto Pallavicini ◽  
Fabrizia Gionechetti ◽  
Francesco Mosca ◽  
...  
Keyword(s):  
Oral Fluid ◽  
Animal Health ◽  
16S Rrna Gene Sequencing ◽  
Research Field ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Bacterial Microbiota ◽  
Lactating Sows ◽  
Original Contribution ◽  
Rrna Gene Sequencing

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs.

Newly introduced Cardinium endosymbiont reduces microbial diversity in the rice brown planthopper Nilaparvata lugens

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Tong-Pu Li ◽  
Si-Si Zha ◽  
Chun-Ying Zhou ◽  
Jun-Tao Gong ◽  
Yu-Xi Zhu ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Developmental Stages ◽  
Brown Planthopper ◽  
16S Rrna Gene Sequencing ◽  
Nilaparvata Lugens ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Intracellular Symbiont ◽  
Acinetobacter Spp ◽  
Rrna Gene Sequencing

ABSTRACT Symbiotic microorganisms in invertebrates play vital roles in host ecology and evolution. Cardinium, a common intracellular symbiont, is transinfected into the important agricultural pest Nilaparvata lugens (rice brown planthopper) to regulate its reproduction, but how this impacts its microbial community is unknown. Here, we characterized the bacterial microbiota from N. lugens, with or without Cardinium, at different developmental stages and in various adult tissues using 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing. Upon infection with Cardinium, we found that microbial diversity in the different developmental stages of N. lugens (especially females), and in female midguts and male testes, was lower than that in the uninfected control. There was a negative correlation between Cardinium and most related genera and between Bacteroidetes and Proteobacteria. Although the microbial structure varied during Cardinium infection, Acinetobacter spp. were a core microbiome genus. The Cardinium infection enhanced the relative density of midgut-associated Acinetobacter spp., with both bacteria exhibiting tissue-specific tropism. In addition, this infection caused the changes of main microbial functions in N. lugens. These results offer insights into the effects of alien (i.e. newly introduced from other organism) Cardinium infection on N. lugens-associated microbiotas, aiding in the development of transinfected endosymbionts for pest control.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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