scholarly journals Characterization of bacterial communities of rhizosphere and rhizoplane of Early Zhukovsky potato

2020 ◽  
Vol 222 ◽  
pp. 02050
Author(s):  
Marat Lutfulin ◽  
Darya Zaripova ◽  
Oksana Moiseeva ◽  
Semen Vologin ◽  
Ayslu Mardanova
Keyword(s):  
Bacterial Communities ◽  
Functional Role ◽  
Agricultural Crop ◽  
Potato Root ◽  
Bacterial Microbiota ◽  
16S R Rna ◽  
Significant Difference ◽  
Dominant Bacteria

Identification of patterns of formation of bacterial communities of the rhizosphere and rhizoplane of potato (Solanum tuberosum L.), the most important agricultural crop, is necessary for the introduction and maintenance of sustainable organic farming. The purpose of this work was the study of the biodiversity of the bacterial microbiota of the rhizosphere and rhizoplane of Early Zhukovsky potato, cultivated on gray forest soils. Comparative analysis based on sequencing of the 16S R RNA gene showed a significant difference in the representation of different groups of bacteria in these potato root compartments. Thus, the proportions of the dominant bacteria in the rhizosphere and rhizoplane of the Proteobacteria phylum reach 47.66% ± 7.22 % and 86.35 % ± 0.53%, respectively (P < 0.05). In contrast, the representation of phylum Bacteroidetes and Firmicutes in the rhizosphere is significantly higher and reaches 41.45 % ± 10.42% and 6.49 % ± 3.23%, respectively, compared to the rhizoplane (7.84 % ± 1.24 % and 0.43 % ± 0.48 %, (P < 0.05). At the same time, Actinobacteria phylum bacteria are present in both compartments in approximately equal amounts (4.40 % ± 1.81% in the rhizosphere and 5.37 % ± 1.42% in the rhizoplane). Thus, it was found that potato forms different bacterial communities in the rhizosphere and rhizoplane in quantitative proportions, which is probably determined by the functional role of these microorganisms in the plant physiology.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

Structural and Thermodynamic Characterization of theEscherichia coliRelBE Toxin−Antitoxin System:  Indication for a Functional Role of Differential Stability†

Biochemistry ◽  
2007 ◽  
Vol 46 (43) ◽  
pp. 12152-12163 ◽  
Author(s):  
Izhack Cherny ◽  
Martin Overgaard ◽  
Jonas Borch ◽  
Yaron Bram ◽  
Kenn Gerdes ◽  
...  
Keyword(s):  
Functional Role ◽  
Thermodynamic Characterization ◽  
Differential Stability

scholarly journals The Close Linkage between Nutrition and Environment through Biodiversity and Sustainability: Local Foods, Traditional Recipes, and Sustainable Diets

2019 ◽  
Vol 11 (10) ◽  
pp. 2876 ◽  
Author(s):  
Alessandra Durazzo
Keyword(s):  
Dietary Patterns ◽  
Functional Role ◽  
Close Correlation ◽  
Close Linkage ◽  
Local Foods ◽  
Special Issue ◽  
Sustainable Diets ◽  
Potential Benefits

This special issue, “The Close Linkage between Nutrition and Environment through Biodiversity and Sustainability: Local Foods, Traditional Recipes, and Sustainable Diets” is focused on the close correlation between the potential benefits and “functional role” of a food and the territory, including papers on the characterization of local foods and traditional recipes, on the promotion of traditional dietary patterns and sustainable diets.

scholarly journals Characterization of the functional role of asp 141, asp 194, and asp464 residues in the Mn2+-l-malate binding of pigeon liver malic enzyme

2008 ◽  
Vol 9 (2) ◽  
pp. 242-251 ◽  
Author(s):  
Wei-Yuan Chou ◽  
Hwei-Ping Chang ◽  
Chien-Hsiun Huang ◽  
Cheng-Chin Kuo ◽  
Gu-Gang Chang ◽  
...  
Keyword(s):  
Malic Enzyme ◽  
Functional Role ◽  
Pigeon Liver

scholarly journals Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases

2015 ◽  
Vol 112 (50) ◽  
pp. E6844-E6851 ◽  
Author(s):  
Grace Caldara-Festin ◽  
David R. Jackson ◽  
Jesus F. Barajas ◽  
Timothy R. Valentic ◽  
Avinash B. Patel ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Functional Role ◽  
Functional Characterization ◽  
Polyketide Synthases ◽  
Type Ii ◽  
Aromatic Polyketides ◽  
Linear Poly ◽  
Bacterial Type

Aromatic polyketides make up a large class of natural products with diverse bioactivity. During biosynthesis, linear poly-β-ketone intermediates are regiospecifically cyclized, yielding molecules with defined cyclization patterns that are crucial for polyketide bioactivity. The aromatase/cyclases (ARO/CYCs) are responsible for regiospecific cyclization of bacterial polyketides. The two most common cyclization patterns are C7–C12 and C9–C14 cyclizations. We have previously characterized three monodomain ARO/CYCs: ZhuI, TcmN, and WhiE. The last remaining uncharacterized class of ARO/CYCs is the di-domain ARO/CYCs, which catalyze C7–C12 cyclization and/or aromatization. Di-domain ARO/CYCs can further be separated into two subclasses: “nonreducing” ARO/CYCs, which act on nonreduced poly-β-ketones, and “reducing” ARO/CYCs, which act on cyclized C9 reduced poly-β-ketones. For years, the functional role of each domain in cyclization and aromatization for di-domain ARO/CYCs has remained a mystery. Here we present what is to our knowledge the first structural and functional analysis, along with an in-depth comparison, of the nonreducing (StfQ) and reducing (BexL) di-domain ARO/CYCs. This work completes the structural and functional characterization of mono- and di-domain ARO/CYCs in bacterial type II polyketide synthases and lays the groundwork for engineered biosynthesis of new bioactive polyketides.

scholarly journals Characterization of glutathione S-transferases from the pine wood nematode, Bursaphelenchus xylophilus

Nematology ◽  
2016 ◽  
Vol 18 (6) ◽  
pp. 697-709 ◽  
Author(s):  
Margarida Espada ◽  
John T. Jones ◽  
Manuel Mota
Keyword(s):  
Post Infection ◽  
Functional Role ◽  
Gland Cell ◽  
Expression Profiles ◽  
Bursaphelenchus Xylophilus ◽  
Pine Wood Nematode ◽  
Glutathione S Transferases ◽  
Pharyngeal Gland

We have previously identified two secreted glutathione S-transferases (GST) expressed in the pharyngeal gland cell of Bursaphelenchus xylophilus, which are upregulated post infection of the host. This study examines the functional role of GSTs in B. xylophilus biology. We analysed the expression profiles of all predicted GSTs in the genome and the results showed that they belong to kappa and cytosolic subfamilies and the majority are upregulated post infection of the host. A small percentage is potentially secreted and none is downregulated post infection of the host. One secreted protein was confirmed as a functional GST and is within a cluster that showed the highest expression fold change in infection. This enzyme has a protective activity that may involve host defences, namely in the presence of terpenoid compounds and peroxide products. These results suggest that GSTs secreted into the host participate in the detoxification of host-derived defence compounds and enable successful parasitism.

scholarly journals Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing

2019 ◽  
Author(s):  
Creciana Maria Endres ◽  
Ícaro Maia Santos de Castro ◽  
Laura Delpino Trevisol ◽  
Michele Bertoni Mann ◽  
Ana Paula Muterle Varela ◽  
...  
Keyword(s):  
Public Health ◽  
16S Rrna ◽  
High Throughput ◽  
Bacterial Communities ◽  
Value Added ◽  
Rrna Gene ◽  
Unifrac Distance ◽  
Organoleptic Characteristics ◽  
Significant Difference

AbstractThe production of sheep’s milk cheese has grown in recent years since it is a high value-added product with excellent properties. As such, it is necessary to provide data on the microbiota and organoleptic characteristics of this product, as well as the influence of these microorganisms on public health. Thus, the aim of the present study was to characterize the microbial community of different types of sheep cheeses using high-throughput sequencing of the 16S rRNA gene. The study was conducted with four groups of cheese: colonial, fresh, feta, and pecorino (n = 5 samples per group). The high-throughput 16S rRNA amplicon sequencing revealed 55 operational taxonomic units in the 20 samples, representing 9 genera of the two bacterial phyla Firmicutes and Proteobacteria. The predominant genera in the samples were Streptococcus and Lactobacillus. When evaluating alpha diversity by the indexes of Simpson, Chao1, Shannon, and Skew no significant differences were observed between the groups. Evaluating of the beta diversity using Bray-Curtis dissimilarity, the group of colonial cheeses presented a significant difference when compared to the feta (q = 0.030) and pecorino groups (q = 0.030). Additionally, the fresh group differed from the pecorino group (q = 0.030). The unweighted Unifrac distance suggests that the colonial cheese group differed from the others. Moreover, the feta cheese group differed from the fresh group. The distance-weighted Unifrac suggests that no significance exists between the groups. According to this information, the microbiota characterization of these cheese groups was useful in demonstrating the bacterial communities belonging to each group, its effects on processing, elaboration, maturation, and public health.

scholarly journals Evaluation of Bacterial Diversity and Quality Features of Traditional Sichuan Bacon from Different Geographical Region

2021 ◽  
Vol 11 (20) ◽  
pp. 9738
Author(s):  
Song Wang ◽  
Xingjie Wang ◽  
Wanshu Pan ◽  
Aiping Liu ◽  
Shuliang Liu ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Physicochemical Characteristics ◽  
Geographical Regions ◽  
Significant Difference ◽  
Geographic Regions ◽  
Shared Otus ◽  
Nitrite Content

Sichuan bacon is one of the most popular types of Chinese bacon in the domestic market. High-throughput sequencing was used to characterize the bacterial diversity of 39 Sichuan bacon samples collected from 3 geographical regions. The results showed that the bacterial diversity of Sichuan bacon in different regions demonstrated certain specificity as well as similarity, and the shared OTUs were close to 81% of the total number in the basin group, mountain group, and plateau group. At the genus level, Staphylococcus is the most dominant genus among the three groups, covering 26.7%, 20.6%, and 22.7%, respectively. Beta diversity shows significant differences in bacterial compositions in different geographic regions, especially for Pseudomonas, Brochothrix, Lactobacillus, Lactococcus, and Enterococcus. Meanwhile, some physicochemical characteristics were analyzed, and a significant difference (p < 0.05) among the three regions was shown in the Aw, pH, and nitrite content, which were significantly correlated with undesired bacteria. This study provides insights into the understanding of the role of bacterial communities in the microbial safety and quality improvement of Sichuan bacon.

scholarly journals Microbiota Dysbiosis in Fungal Rhinosinusitis

2019 ◽  
Vol 8 (11) ◽  
pp. 1973 ◽  
Author(s):  
Yen-Ting Lu ◽  
Shao-Hung Wang ◽  
Ming-Li Liou ◽  
Ting-An Shen ◽  
Ying-Chou Lu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Chronic Rhinosinusitis ◽  
Bacterial Communities ◽  
Middle Meatus ◽  
Fungal Rhinosinusitis ◽  
Bacterial Microbiota ◽  
Histological Characteristics ◽  
Distinct Distribution

Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.

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