scholarly journals Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Elisa C. P. Catão ◽  
Fabyano A. C. Lopes ◽  
Janaína F. Araújo ◽  
Alinne P. de Castro ◽  
Cristine C. Barreto ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Atlantic Forest ◽  
Phylogenetic Reconstruction ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Cerrado Vegetation ◽  
Starting Point ◽  
Rrna Sequences ◽  
16S Rrna Sequences

16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in “Mata de galeria” forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al3+concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored.

scholarly journals Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

2021 ◽  
Vol 12 ◽  
Author(s):  
Marc Crampon ◽  
Coralie Soulier ◽  
Pauline Sidoli ◽  
Jennifer Hellal ◽  
Catherine Joulian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Treated Wastewater ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

scholarly journals Evidence and molecular characterization ofBartonellaspp. and hemoplasmas in neotropical bats in Brazil

2017 ◽  
Vol 145 (10) ◽  
pp. 2038-2052 ◽  
Author(s):  
P. IKEDA ◽  
M. C. SEKI ◽  
A. O. T. CARRASCO ◽  
L. V. RUDIAK ◽  
J. M. D. MIRANDA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Clinical Manifestations ◽  
Rrna Gene ◽  
Zoonotic Virus ◽  
The World ◽  
Neotropical Bats ◽  
Latin America Countries ◽  
Rrna Sequences ◽  
16S Rrna Sequences

SUMMARYThe order Chiroptera is considered the second largest group of mammals in the world, hosting important zoonotic virus and bacteria.Bartonellaand hemotropic mycoplasmas are bacteria that parasite different mammals’ species, including humans, causing different clinical manifestations. The present work aimed investigating the occurrence and assessing the phylogenetic positioning ofBartonellaspp. andMycoplasmaspp. in neotropical bats sampled from Brazil. Between December 2015 and April 2016, 325 blood and/or tissues samples were collected from 162 bats comprising 19 different species sampled in five states of Brazil. Out of 322 bat samples collected, while 17 (5·28%) were positive to quantitative PCR forBartonellaspp. based onnuoGgene, 45 samples (13·97%) were positive to cPCR assays for hemoplasmas based on 16S rRNA gene. While seven sequences were obtained forBartonella(nuoG) (n= 3),gltA(n= 2),rpoB(n= 1),ftsZ(n= 1), five 16S rRNA sequences were obtained for hemoplasmas. In the phylogenetic analysis, theBartonellasequences clustered withBartonellagenotypes detected in bats sampled in Latin America countries. All five hemoplasmas sequences clustered together as a monophyletic group by Maximum Likelihood and Bayesian Inference analyses. The present work showed the first evidence of circulation ofBartonellaspp. and hemoplasmas among bats in Brazil.

scholarly journals Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
M. Idnan ◽  
A. Javid ◽  
M. Tayyab ◽  
A. Hussain ◽  
S. Mansoor ◽  
...  
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Molecular Identification ◽  
Dna Sequences ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Morphometric Measurements ◽  
Tree Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Abstract A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.

scholarly journals Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Abeer Babiker Idris ◽  
Hadeel Gassim Hassan ◽  
Maryam Atif Salaheldin Ali ◽  
Sulafa Mohamed Eltaher ◽  
Leena Babiker Idris ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Human Migration ◽  
Rrna Gene ◽  
Migration Patterns ◽  
H Pylori ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Background. Helicobacter pylori (H. pylori) is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of H. pylori strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. Materials and methods. A total of 75 gastric biopsies were taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was performed by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. The evolutionary aspects were analyzed using MEGA7 software. Results. Molecular detection of H. pylori has shown that 28 (37.33%) of the patients were positive for H. pylori and no significant differences were found in sociodemographic characteristics, endoscopy series, and H. pylori infection. Nucleotide variations were observed at five nucleotide positions (positions 219, 305, 578, 741, and 763–764), and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. These six mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites; 66.67% of them were located in the central domain of 16S rRNA. The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. The presence of Sudanese H. pylori strains resembling Hungarian H. pylori strains could reflect the migration of Hungarian people to Sudan or vice versa. Conclusion. This finding emphasizes the significance of studying the phylogeny of H. pylori strains as a discriminatory tool to mirror human migration patterns. In addition, the 16S rRNA gene amplification method was found useful for bacterial identification and phylogeny.

scholarly journals First insights into molecular basis identification of 16 s ribosomal RNA gene of Staphylococcus aureus isolated from Sudan

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Manal A. Gumaa ◽  
Abeer Babiker Idris ◽  
N. E. Bilal ◽  
Mohamed A. Hassan
Keyword(s):  
Staphylococcus Aureus ◽  
16S Rrna ◽  
Ribosomal Rna ◽  
Molecular Basis ◽  
Molecular Detection ◽  
Rrna Gene ◽  
Wound Infections ◽  
Resistant Phenotype ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Abstract Objective In this study, we analyzed the molecular evolution of Staphylococcus aureus isolates using 16S rRNA gene and phylogenetic analysis to detect the prevalence of S. aureus infections in Sudan. Results Molecular detection of S. aureus has shown that 20 (43.47%) of patients were positive for S. aureus. The phylogenetic tree of 16S rRNA sequences was divided into three lineages of S. aureus isolates detected from wound infections in Sudan. Nucleotides base-pair substitution was appeared at position 249. This mutation do not linked with Macrolides, Lincosamides and Streptogramines b resistant phenotype. Further studies should investigate the effect of that mutation on resistance to other antibiotics.

scholarly journals Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment

2020 ◽  
Author(s):  
Megan Sarah Beaudry ◽  
Jincheng Wang ◽  
Troy Kieran ◽  
Jesse Thomas ◽  
Natalia Juliana Bayona-Vasquez ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
16S Rrna Sequence ◽  
Shotgun Metagenomics ◽  
Reference Databases ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases. However, shotgun metagenomic sequencing is much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having < 80% sequence similarity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average >400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely in part to the extent and curation of the reference databases considered.

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs

2015 ◽  
Vol 11 (7) ◽  
pp. 1907-1913 ◽  
Author(s):  
Ze-Gang Wei ◽  
Shao-Wu Zhang
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput ◽  
Hierarchical Method ◽  
Rapid Accumulation ◽  
Rrna Sequences ◽  
Recent Sequencing ◽  
16S Rrna Sequences

The recent sequencing revolution driven by high-throughput technologies has led to rapid accumulation of 16S rRNA sequences for microbial communities.

scholarly journals Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments

2011 ◽  
Vol 77 (15) ◽  
pp. 5529-5532 ◽  
Author(s):  
Antonio Del Casale ◽  
Paul V. Flanagan ◽  
Michael J. Larkin ◽  
Christopher C. R. Allen ◽  
Leonid A. Kulakov
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Total Bacterial Community ◽  
Rrna Sequences ◽  
16S Rrna Sequences ◽  
Bacterial 16S Rrna Gene

ABSTRACTPhage metagenomes isolated from wastewater over a 12-month period were analyzed. The results suggested that various strains ofProteobacteria,Bacteroidetes, and other phyla are likely to participate in transduction. The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community.

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