scholarly journals Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

2006 ◽  
Vol 41 (10) ◽  
pp. 1507-1516 ◽  
Author(s):  
Érico Leandro da Silveira ◽  
Rodrigo Matheus Pereira ◽  
Denilson César Scaquitto ◽  
Eliamar Aparecida Nascimbém Pedrinho ◽  
Silvana Pómpeia Val-Moraes ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Chemical Properties ◽  
Pcr Primers ◽  
Native Forest ◽  
Sequencing Analysis ◽  
Soil Dna ◽  
Rdna Sequencing ◽  
The Impact

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

scholarly journals Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Relvas ◽  
A. Regueira-Iglesias ◽  
C. Balsa-Castro ◽  
F. Salazar ◽  
J. J. Pacheco ◽  
...  
Keyword(s):  
Oral Health ◽  
Periodontal Disease ◽  
Bacterial Diversity ◽  
Predictive Models ◽  
Oral Disease ◽  
Rrna Gene ◽  
Convenience Sample ◽  
Core Microbiome ◽  
Rdna Sequencing ◽  
The Impact

AbstractThe present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

Identification of Photobionts from the lichen family Physciaceae using algal-specific ITS rDNA sequencing

2001 ◽  
Vol 33 (1) ◽  
pp. 73-86 ◽  
Author(s):  
Gert Helms ◽  
Thomas Friedl ◽  
Gerhard Rambold ◽  
Helmut Mayrhofer
Keyword(s):  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Its Rdna ◽  
Generic Level ◽  
Sequence Comparisons ◽  
Its Phylogeny ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
Geographical Regions

AbstractThe identity of photobionts from 20 species of the Physciaceae from different habitats and geographical regions has been determined by ITS rDNA sequence comparisons in order to estimate the diversity of photobionts within that lichen group, to detect patterns of specificity of mycobionts towards their photobionts and as a part of an ongoing study to investigate possible parallel cladogenesis of both symbionts. Algal-specific PCR primers have been used to determine the ITS rDNA sequences from DNA extractions of dried lichens that were up to 5 years old. Direct comparisons and phylogenetic analyses allowed the assignment of Physciaceae photobionts to four distinct clades in the photobiont ITS rDNA phylogeny. The results indicate a diversity within the genus Trebouxia Puymaly and Physciaceae photobionts that is higher than expected on the basis morphology alone. Physciaceae photobionts belonged to 12 different ITS lineages of which nine could unambiguously be assigned to six morphospecies of Trebouxia. The identity of the remaining three sequences was not clarified; they may represent new species. Specificity at the generic level was low as a whole range of photobiont species were found within a genus of Physciaceae and different ranges were detected. The photobionts of Physcia (Schreb.) Michaux were closely related and represented one morphospecies of Trebouxia, whereas the algal partners of Buellia De Not and Rinodina (Ach.) Gray were in distant lineages of the ITS phylogeny and from several Trebouxia morphospecies. Photobiont variation within a genus of Physciaceae may be due to phylogeny, geographical distance or because photobionts from neighbouring lichens were taken (“algal sharing“). At the species level Physciaceae mycobionts seem to be rather selective and contained photobionts that were very closely related within one morphospecies of Trebouxia.

Identification ofEnterococcus sp. from midgut of silkworm based on biochemical and 16S rDNA sequencing analysis

2006 ◽  
Vol 56 (3) ◽  
pp. 201-205 ◽  
Author(s):  
Chen Fei ◽  
Xing-meng Lu ◽  
Yong-hua Qian ◽  
Haiyan Zhang ◽  
Qaisar Mahmood
Keyword(s):  
16S Rdna ◽  
Sequencing Analysis ◽  
16S Rdna Sequencing ◽  
Rdna Sequencing

scholarly journals Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy

2015 ◽  
Vol 37 (3) ◽  
pp. 251 ◽  
Author(s):  
Raphael Barbetta de Jesus ◽  
Wellington Pine Omori ◽  
Eliana Gertrudes De Macedo Lemos ◽  
Jackson Antônio Marcondes de Souza
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
16S Rdna Sequencing ◽  
Bovine Rumen ◽  
Rdna Sequencing ◽  
Scanning Electron

Unraveling metabolically active fungal-bacterial diversity in commercial organic vineyard soils

2020 ◽  
Author(s):  
Carmen Biel ◽  
Miriam Guivernau ◽  
Marc Viñas ◽  
Xavier Aranda ◽  
Felicidad de Herralde
Keyword(s):  
Bacterial Diversity ◽  
Fungal Diversity ◽  
Sandy Loam ◽  
Soil Depth ◽  
Sequencing Analysis ◽  
Fungal Population ◽  
Post Harvest ◽  
Bloom Period ◽  
Vineyard Soils ◽  
The Impact

<p>This study aims to assess the impact of the pre-bloom and post-harvest periods on the diversity of metabolically active soil-rhizosphere microbiota in a commercial vineyard in Sant Sadurní d’Anoia, a typical wine producing region (Penedès DO, Catalonia, Spain). Thereby, total genomic DNA and RNA was simultaneously monitored to distinguish total from active bacterial-fungal microbiota, by molecular tools in both periods. The studied organic vineyard had 20 years old plants of the white grape variety of Macabeu and 41B as a rootstock. Soil had last been amended (14 tm/ha of composted cow manure) 5 years before.</p><p>The soil was monitored in April 2018 in the pre-bloom period (stages 09 to 12 Eichhorn and Lorenz 1977) and the post-harvest period (October 2018) in 2 different plots of the vineyard: Zone1 (loam texture with permanent cover crop) and Zone 4 (sandy-loam without vegetal cover). Samples soils were obtained at a soil depth of30 cm and 20 cm of distance from a plant (n=4 for each plot and sampling event). Each soil sample was submerged in a DNA/RNA preservative solution at 4⁰C and afterward stored at -20⁰C until the further analysis. In order to quantify and to assess bacterial and fungal diversity (total and active), (RT)qPCR and MiSeq-Illumina analysis (16SrRNA/ITS1rRNA region) were performed.</p><p>Results showed that in post-harvest period the bacterial populations were more active in both zones (2 and 5 orders of magnitude in Zone1 and Zone4, respectively) vs. pre-bloom period. Metabolically active fungal population was increased in both plots by 4 orders of magnitude. It is noteworthy to mention that fungal population was present but not active in pre-harvest period. This fact could be explained for the mutualistic microbe interaction and the environmental conditions (soil temperature and soil water content), including grape drop in harvest linked to rainy conditions.</p><p>High-throughput sequencing analysis revealed that the microbial diversity was specific for each plot, vine and sampling period. Bacterial population in post-harvest was more diversified but still dominated by Actinobacteria (mainly by Actinomycetales order), Proteobacteria (mainly by Rhizobiales and Pseudomonadales orders). Interestingly, during post-harvest Clostridiales (Firmicutes phylum), present in the pre-bloom period, completely disappeared. Alpha bacterial diversity was higher than fungal one in both plots. Interestingly, the bacterial diversity (H Shannon index) of metabolically active bacteria (cDNA) was higher during post-harvest season compared to April, suggesting more activity and diversity in the former. On the contrary, fungal diversity was smaller and less uniform in both periods. They were predominated by Ascomycota, Basidiomycota and Zygomycota phyla. Noticeably, the relative abundance (RA) of existing fungal population (DNA) in the soil were highly different compared to the RA of active fungal community (cDNA).</p><p>In conclusion, simultaneous RNA/DNA-based molecular biology tools could improve the knowledge of metabolically active microbial populations in vineyard soils under different seasons.</p><p>Funding: VITIMPAC project (INIA RTA2015-00091-00-00).</p>

Physiological and genetic characterization of fluorescentPseudomonasassociated withCantharellus cibarius

2002 ◽  
Vol 48 (8) ◽  
pp. 739-748 ◽  
Author(s):  
J Ignacio Rangel-Castro ◽  
Jolanta J Levenfors ◽  
Eric Danell
Keyword(s):  
16S Rdna ◽  
Fungal Mycelium ◽  
Sequencing Analysis ◽  
Carbon Utilization ◽  
Pseudomonas Spp ◽  
Fluorescent Pseudomonas ◽  
Rdna Sequencing ◽  
Pcr Rflp ◽  
Polymerase Chain

Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed physiologically from isolates from soil lacking FB and had some similarities with the strains obtained from soil underneath the FB. Analyses of the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) patterns and partial sequencing analysis of the 16S-rDNA region indicated that the bacteria isolated from these environments were different. However, there was no specific Pseudomonas genotype restricted to the FB environment. Utilization of the reported fungal exudates trehalose and mannitol may explain how millions of bacteria survive in the C. cibarius FB without deteriorating the fungal mycelium. The importance of the metabolic characterization of bacteria and the possible mechanisms involved in the association with C. cibarius are discussed. Our study showed that standard processes for bacterial identification, e.g., Biolog®and 16S-rDNA are insufficient until databases for different ecosystems are created.Key words: Cantharellus cibarius, fluorescent Pseudomonas, carbon utilization, PCR–RFLP, 16S-rDNA sequencing.

scholarly journals Characterization of Microbial Communities in a Dairy Farm Matrix in Ningxia, China, by 16S rDNA Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Wen Zhang ◽  
Wu Li ◽  
Chenjie Ma ◽  
Xiaoling Wu ◽  
Xunde Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Dairy Farm ◽  
Dairy Manure ◽  
Zoonotic Pathogens ◽  
Rdna Sequencing ◽  
The Impact

A large amount of dairy manure is produced annually in the Ningxia Hui Autonomous Region of China due to the increase in food-producing animal agriculture in this region. The presence of bovine-originated zoonotic, especially human, pathogenic bacteria in untreated manure poses a significant threat to the environment and to public health. However, little is known about the composition, diversity, and abundance of bacterial communities in untreated dairy manure in the Ningxia region. In this study, the microbial community structure of the dairy farm matrix was characterized through 16S rDNA sequencing. The impact of manure treatment methods on bacterial communities was also analyzed. The results showed that the microbial community in dairy manure contained both beneficial bacteria and pathogens, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Actinobacteria as dominant phyla. The results also showed the diversity and variety of abundance of zoonotic pathogens among different matrices. The number of pathogens was found to increase significantly in the accumulated but untreated manure, which appeared to be the main matrix of dairy farms that accumulated pathogens including zoonotic pathogens. Findings from this study suggested that farm management, particularly proper treatment of manure, is essential to achieve a shift in the bacterial community composition and a reduction in the environmental load of pathogens including zoonotic pathogens.

scholarly journals Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

1998 ◽  
Vol 64 (11) ◽  
pp. 4333-4339 ◽  
Author(s):  
Daniel H. Buckley ◽  
Joseph R. Graber ◽  
Thomas M. Schmidt
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Long Term Ecological Research

ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

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