scholarly journals Updating the resolution for 16S rRNA OTUs clustering reveals the cryptic cyanobacterial genus and species

2020 ◽  
Vol 117 ◽  
pp. 106695 ◽  
Author(s):  
Xiaochuang Li ◽  
Shouliang Huo ◽  
Beidou Xi
Keyword(s):  
16S Rrna ◽  
Cyanobacterial Genus

16S rRNA GENE HETEROGENEITY IN THE FILAMENTOUS MARINE CYANOBACTERIAL GENUS LYNGBYA1

2010 ◽  
Vol 46 (3) ◽  
pp. 591-601 ◽  
Author(s):  
Niclas Engene ◽  
R. Cameron Coates ◽  
William H. Gerwick
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Cyanobacterial Genus

scholarly journals Establishment of a New Filamentous Cyanobacterial Genus, Microcoleusiopsis gen. nov. (Microcoleaceae, Cyanobacteria), from Benthic Mats in Open Channel, Jiangxi Province, China

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 548
Author(s):  
Ruozhen Geng ◽  
Wenke Li ◽  
Aimin Chao ◽  
Xiaoyu Guo ◽  
Hua Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Secondary Structures ◽  
16S Rrna Gene Sequence ◽  
Jiangxi Province ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cyanobacterial Genus

Cyanobacterial taxonomic studies performed by using the modern approaches always lead to creation of many new genera and species. During the field survey for cyanobacterial resources in China, a filamentous cyanobacterial strain was successfully isolated from a microbial mat attached to rock surfaces of the Ganfu Channel, Jiangxi Province, China. This strain was morphologically similar to the cyanobacterial taxa belonging to the genera Microcoleus and Phormidium. The phylogenetic analyses based on 16S rRNA gene sequences showed that this strain formed a well-supported clade, close to the filamentous genera Microcoleus, Tychonema, and Kamptonema. The maximum similarity of 16S rRNA gene sequence of this strain with the related genera was 95.04%, less than the threshold for distinguishing bacterial genus. The ITS secondary structures also distinguish this strain from the related cyanobacterial genera. Therefore, combined with morphology, 16S rRNA gene sequence, and ITS secondary structures, a novel cyanobacterial genus here as Microcoleusiopsis was established, with the species type as Microcoleusiopsis ganfuensis.

scholarly journals Detection of Toxigenicity by a Probe for the Microcystin Synthetase A Gene (mcyA) of the Cyanobacterial Genus Microcystis: Comparison of Toxicities with 16S rRNA and Phycocyanin Operon (Phycocyanin Intergenic Spacer) Phylogenies

2001 ◽  
Vol 67 (6) ◽  
pp. 2810-2818 ◽  
Author(s):  
Daniel Tillett ◽  
Dorothy L. Parker ◽  
Brett A. Neilan
Keyword(s):  
16S Rrna ◽  
Protein Phosphatase ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
Microcystin Synthetase ◽  
Field Samples ◽  
Protein Phosphatase Inhibition ◽  
Phosphatase Inhibition ◽  
Cyanobacterial Genus

ABSTRACT The relationship between toxigenicity and phylogeny within the cyanobacterial genus Microcystis is unclear. To investigate this issue, we have designed PCR primers for theN-methyltransferase (NMT) domain of the microcystin synthetase gene mcyA and have probed 37Microcystis sp. cultures as well as several field samples. The NMT region was present in all 18 laboratory strains that gave positive reactions in the protein phosphatase inhibition assay for microcystin but was absent in 17 nontoxic strains. Two other nontoxic strains, one of which had previously been reported to produce microcystin, possessed the NMT region. Detection of NMT-specific DNA in field samples corresponded to periods of toxicity as assessed by protein phosphatase inhibition. The Microcystis strains formed a monophyletic cluster based on 16S rRNA gene sequences but comprised two groups with respect to phycocyanin intergenic spacer (PC-IGS) sequences. Toxic and nontoxic strains appeared to be erratically distributed within the PC-IGS and 16S rRNA trees. Sequence analysis of the NMT domain revealed two coherent groups. The genomic region immediately downstream of the mcyABC cluster in all 20 NMT-positive strains contained an open reading frame of unknown function (uma1) at a conserved distance frommcyC. All nontoxic strains also containeduma1, which is not cotranscribed withmcyABC. The consistent linkage of mcyC touma1 suggests that mcyC has not been frequently transferred into nontoxic strains via any mechanism involving insertion at random chromosomal locations. These results are discussed with respect to various mechanisms that could explain the patchy distribution of toxigenicity among the variousMicrocystis clades.

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Haemophilus parainfluenzaeInfective Endocarditis Diagnosed by Direct 16S rRNA Sequencing of Vegetation

2012 ◽  
Vol 2 (2) ◽  
pp. 111
Author(s):  
Sung-Hee Oh ◽  
Min-Chul Cho ◽  
Jae-Wook Kim ◽  
Dongheui An ◽  
Mun-Hui Jeong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Sequencing ◽  
Rrna Sequencing

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

ISOLASI, SELEKSI, DAN IDENTIFIKASI BAKTERI SELULOLITIK DARI RUMPUT LAUT Turbinaria sp. DAN Sargassum sp. SEBAGAI KANDIDAT PENDEGRADASI SERAT KASAR PAKAN IKAN

2015 ◽  
Vol 10 (1) ◽  
pp. 51
Author(s):  
Mulyasari Mulyasari ◽  
Irma Melati ◽  
Mas Tri Djoko Sunarno
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna

Kecernaan karbohidrat oleh ikan dapat ditingkatkan antara lain melalui penambahan bakteri selulolitik dalam pakan. Salah satu sumber bakteri selulolitik adalah rumput laut. Oleh karena itu, suatu penelitian dilakukan dengan tujuan untuk mendapatkan bakteri selulolitik dari rumput laut Turbinaria sp. dan Sargassum sp. Bakteri selulolitik diisolasi dengan metode pengenceran, streaking dan spreading pada media carboxymethylcellulose (CMC). Koloni yang didapat dimurnikan dan diseleksi dengan menggunakan uji aktivitas enzim selulase secara kualitatif (zona bening) dan kuantitatif, serta diidentifikasi secara biokimia dan molekuler menggunakan gen 16S-rRNA. Pada penelitian ini diperoleh 22 isolat murni bakteri dengan dua isolat yang mempunyai aktivitas selulolitik tertinggi, yaitu TS2b dan SS4b. Hasil uji biokimia dan karakterisasi secara molekuler menunjukkan bahwa kedua isolat tersebut adalah Bacillus subtilis dan B. megaterium.

Sign in / Sign up

Export Citation Format

Share Document