Phylogenetic assessment of five filamentous bacteria isolated from bulking activated sludges

1998 ◽  
Vol 37 (4-5) ◽  
pp. 303-306 ◽  
Author(s):  
R. Howarth ◽  
I. M. Head ◽  
R. F. Unz
Keyword(s):  
Ribosomal Rna ◽  
Oligonucleotide Probe ◽  
Strong Relationship ◽  
Bootstrap Support ◽  
Its Sequence ◽  
Target Sequence ◽  
Common Ancestry ◽  
Filamentous Bacteria ◽  
Axenic Strains ◽  
Rrna Sequences

Nearly complete 16S ribosomal RNA (rRNA) sequences were determined for fully characterised axenic strains of Thiothrix, Eikelboom type O21N, and Eikelboom type 1701 originally isolated from bulking activated sludges. Thiothrix strains formed a monophyletic group (100% bootstrap support) with previously described Thiothrix nivea strain JP2 and Thiothrix ramosa. Eikelboom type O21N strain AP3 revealed a sufficiently strong relationship to the Thiothrix group to suggest a common ancestry for the two organism although it was not possible to designate type 021N as a species of Thiothrix. Eikelboom type 1701 contained within its sequence the target sequence of an oligonucleotide probe for the detection of Sphaerotilus natans.

Group I Intron Versus its Sequences in Phylogeny of Cetrarioid Lichens

1999 ◽  
Vol 31 (5) ◽  
pp. 441-449 ◽  
Author(s):  
Arne Thell
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Group I Intron ◽  
Ribosomal Genes ◽  
Its Sequences ◽  
Its Sequence ◽  
Ribosomal Rna Gene ◽  
18S Ribosomal Rna Gene ◽  
Group I

AbstractPhylogenetic trees based on group I intron sequences and on internal transcribed spacer (ITS) sequences of mycobiont ribosomal genes were calculated and compared. Eight cetrarioid and four non-cetrarioid species of the Parmeliaceae were compared. The phylogeny based on group I intron sequences is partly congruent with the ITS sequence phylogeny. Group I intron sequences are presumably less informative for infragenic studies. The introns have a length of 214–233 nucleotides, and differ at up to 33% of the bases between species. All introns analysed are located between the positions 1516 and 1517 of the fungal 18S ribosomal RNA gene. Cetrarioid lichens form a non-homogeneous group within the Parmeliaceae according to both group I intron and ITS sequences.

scholarly journals Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

2018 ◽  
Author(s):  
Marine Lambert ◽  
Abderrahim Benmoussa ◽  
Patrick Provost
Keyword(s):  
Ribosomal Rna ◽  
Potential Role ◽  
A Priori ◽  
Biological Significance ◽  
Rna Seq ◽  
New Class ◽  
Scientific Mind ◽  
Non Coding Rnas ◽  
And Function ◽  
Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

scholarly journals Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Middle Portion ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. Results Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. Conclusion The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

Application of oligonucleotide probes for the detection of Thiothrix spp. in activated sludge plants treating paper and board mill wastes

2002 ◽  
Vol 46 (1-2) ◽  
pp. 559-564 ◽  
Author(s):  
S.B. Kim ◽  
M. Goodfellow ◽  
J. Kelly ◽  
G.S. Saddler ◽  
A.C. Ward
Keyword(s):  
Activated Sludge ◽  
Bacterial Population ◽  
Oligonucleotide Probe ◽  
In Situ Hybridisation ◽  
Filamentous Bacteria ◽  
Phylogenetic Groups ◽  
Investigation Period ◽  
Mixed Populations ◽  
Conventional Microscopy

Filamentous bacteria belonging to the genus Thiothrix were detected in activated sludge samples using the fluorescent in situ hybridisation (FISH) technique. A 16S rRNA-targeted oligonucleotide probe was developed for the detection of members of the T. fructosivorans group, and the performance of probe TNI for the detection of Thiothrix nivea group was enhanced by using an unlabeled competitor. A set of 5 probes covering all phylogenetic groups of Thiothrix were used to examine samples taken from selected activated sludge plants treating paper and board mill wastes. Members of the T. eikelboomii group formed the predominant filamentous bacterial population in plants experiencing poor sludge settleability, whereas members of the T. nivea group were commonly found but not dominantly in the remaining plants. Members of the T. fructosivorans group were not detected at any significant level in any of the samples. The distribution of the main Thiothrix types remained unchanged throughout the investigation period. It was evident that mixed populations of Thiothrix spp. were present in all activated sludge samples investigated, the observed differences were in the relative abundance of the various groups. These findings were supported by the results obtained using conventional microscopy.

scholarly journals A Preliminary Phylogeny of Rhyacophilidae with Reference to Fansipangana and the Monophyly of Rhyacophila

Zoosymposia ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. 189-192
Author(s):  
JULIANNE E. MCLAUGHLIN ◽  
PAUL B. FRANDSEN ◽  
WOLFRAM MEY ◽  
STEFFEN U. PAULS
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Ribosomal Rna ◽  
Additional Data ◽  
Sister Taxon ◽  
Bootstrap Support ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Data Set ◽  
Extensive Data

The phylogeny of Rhyacophilidae was explored with 28S ribosomal RNA (rRNA) and Cytochrome Oxidase Subunit I (COI) mitochondrial DNA (mtDNA). Eighty one rhyacophilids were included in the analysis. We found that although Rhyacophilidae was recovered as monophyletic, intrafamilial relationships are not well-resolved using this dataset. Bootstrap support was poor for intrageneric relationships and additional data will be required to present a more robust hypothesis. The recovered phylogeny places Fansipangana as the sister taxon of the rest of Rhyacophilidae. We found that Himalopsyche was nested inside the genus Rhyacophila with the verrula group sister to Himalopsyche and remaining Rhyacophila. These results and possible relationships should be tested with a more extensive data set.

scholarly journals Phylogenetic Analysis of and Oligonucleotide Probe Development for Eikelboom Type 021N Filamentous Bacteria Isolated from Bulking Activated Sludge

2000 ◽  
Vol 66 (11) ◽  
pp. 5043-5052 ◽  
Author(s):  
Takahiro Kanagawa ◽  
Yoichi Kamagata ◽  
Shinobu Aruga ◽  
Tetsuro Kohno ◽  
Matthias Horn ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Oligonucleotide Probe ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
Filamentous Bacteria ◽  
16S Rdna Sequence ◽  
Monophyletic Cluster ◽  
16S Ribosomal Dna ◽  
In Situ Detection

ABSTRACT Fifteen filamentous strains, morphologically classified as Eikelboom type 021N bacteria, were isolated from bulking activated sludges. Based on comparative 16S ribosomal DNA (rDNA) sequence analysis, all strains form a monophyletic cluster together with all recognized Thiothrix species (88.3 to 98.7% 16S rDNA sequence similarity) within the gamma-subclass ofProteobacteria. The investigated Eikelboom type 021N isolates were subdivided into three distinct groups (I to III) demonstrating a previously unrecognized genetic diversity hidden behind the uniform morphology of the filaments. For in situ detection of these bacteria, 16S rRNA-targeted oligonucleotide probes specific for the entire Eikelboom type 021N-Thiothrix cluster and the Eikelboom type 021N groups I, II, and III, respectively, were designed, evaluated, and successfully applied in activated sludge.

Oligonucleotide probes based on 16S rRNA sequences for the identification of four Azospirillum species

1995 ◽  
Vol 41 (12) ◽  
pp. 1081-1087 ◽  
Author(s):  
Md Mahbubul Kabir ◽  
Denis Faure ◽  
Jacqueline Haurat ◽  
Philippe Normand ◽  
René Bally ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oligonucleotide Probe ◽  
Oligonucleotide Probes ◽  
Probe Sequence ◽  
Bacterial Isolation ◽  
Nontarget Organisms ◽  
Isolation Techniques ◽  
Species Specific ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.Key words: Azospirillum, bacterial isolation, hybridization, oligonucleotide probe, sequence analysis, 16S rRNA.

The nuclear small subunit ribosomal genes of Sphaeronaemella helvellae, Sphaeronaemella fimicola, Gabarnaudia betae, and Cornuvesica falcata: phylogenetic implications

2004 ◽  
Vol 82 (6) ◽  
pp. 752-762 ◽  
Author(s):  
Georg Hausner ◽  
James Reid
Keyword(s):  
Ribosomal Rna ◽  
Sequence Data ◽  
Small Subunit ◽  
Ribosomal Genes ◽  
Phylogenetic Position ◽  
Ophiostomatoid Fungi ◽  
Original Material ◽  
Common Ancestry ◽  
Phylogenetic Implications ◽  
Rna Genes

Sequences were obtained from the nuclear small subunit ribosomal RNA genes for representatives of four ophiostomatoid genera (Ceratocystis, Gondwanamyces, Cornuvesica, and Sphaeronaemella) to resolve their phylogenetic position within the Ascomycota. Phylogenetic analysis suggests that these genera are monophyletic and share common ancestry with members of the Microascales. Based on sequence data, strains representing the mitotic species Gabarnaudia betae (Delacr.) Samson & W. Gams were shown clearly to be derived from Sphaeronaemella species. Sequences were also obtained from strains representing the syntype of Sphaeronaemella fragariae, the exholotype of Sphaeronaemella humicola, and the extype of Gabarnaudia tholispora. The results suggest that putative extype cultures for S. humicola and G. tholispora no longer represent the original material deposited. Our data also support the exclusion of S. fragariae from Sphaeronaemella. Key words: Cornuvesica, Gabarnaudia, Gondwanamyces, Sphaeronaemalla fragariae, ophiostomatoid fungi, ribosomal DNA.

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