Molecular Phylogenetic study of Acila divaricata vigila based on the Partial Sequence of 16S rRNA Gene

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

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Molecular phylogenetic study of rare weed-field species of the genus Avena L.

Проблемы ботаники Южной Сибири и Монголии ◽

10.14258/pbssm.2021022 ◽

2021 ◽

Vol 20 (1) ◽

pp. 108-111

Author(s):

A. A. Gnutikov ◽

N. N. Nosov ◽

I. G. Loskutov ◽

E. V. Blinova ◽

A. V. Rodionov

Keyword(s):

Phylogenetic Study ◽

Rrna Gene ◽

Its1 Sequence ◽

5.8S Rrna Gene ◽

Molecular Phylogenetic Study ◽

5.8S Rrna ◽

C Genome ◽

Molecular Phylogenetic ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those associated with the C-genome were not found. The presence of unique ribotypeswas shown for A. persica and A. georgica.

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Oxynema aestuarii sp. nov. (Microcoleaceae) isolated from an Indian mangrove forest

Phytotaxa ◽

10.11646/phytotaxa.374.1.2 ◽

2018 ◽

Vol 374 (1) ◽

pp. 24 ◽

Cited By ~ 2

Author(s):

SANDEEP CHAKRABORTY ◽

VEERABADHRAN MARUTHANAYAGAM ◽

ANUSHREE ACHARI ◽

RIDDHI MAHANSARIA ◽

ARNAB PRAMANIK ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Hypersaline Environment ◽

Phylogenetic Study ◽

Rrna Gene ◽

Growth Responses ◽

Nucleotide Substitutions ◽

Intertidal Environment ◽

Group I

Taxonomic characterization by a polyphasic approach was carried out on two cyanobacteria, AP17 and AP24 isolated from soil biofilms of two separate islands, Lothian and Sagar respectively, of the Indian Sundarbans. The strains were studied morphologically by light microscopy, scanning and transmission electron microscopy. Growth responses to various salinities were recorded. Molecular data included sequencing and phylogenetic study of the 16S rRNA gene as well as analysis of the 14 regions of the 16S-23S ITS regions. Morphologically the strains were found to be non-heterocytous, having attenuated trichomes with a narrow, bent terminal cell without any crosswalls. Strains under investigation shared 99–100% 16S rRNA gene sequence similarity with Oxynema thaianum CCALA960, the type species of the novel Oxynema genus, recently separated from the Phormidium-Group I genus. However, cross walls in the apical portion of AP17 and AP24 were totally absent while the same was present in CCALA960. Additionally, optimal growth of AP17 and AP24 was recorded in 5–8% salinity and salinity above 14% inhibited growth of both strains, which were isolated from an intertidal environment; whereas O. thaianum CCALA960 which was found in a hypersaline environment could grow at 40% salinity. Insertion of 9 nucleotides in the D2 with spacer region, insertion of 2 nucleotides in the pre Box B spacer region, deletion of 2 nucleotides in the post Box B spacer region, deletion of 8 nucleotides in the D4 region, deletion of 8 nucleotides in V3 region and insertion of 2 nucleotides in the D5 region of the ITS sequences of AP17 and AP24 were observed in comparison to the analogous regions of CCALA960. Structural details of Box B helices of AP17 and AP24 revealed that although their lengths were identical with the reference, their sequences were completely different from CCALA960. Four nucleotide substitutions were observed in different positions in the Box B helix of O. thaianum CCALA960. Secondary structures of the V3 regions of AP17 and AP24 (containing 51 nucleotides) showed a small terminal bulge and a bigger bilateral bulge while the analogous structure of O. thaianum CCALA 960 (comprising of 59 nucleotides) showed one additional bilateral bulge in comparison to AP17 and AP24. Therefore, based on morphological, ecological and molecular differences in comparison to O. thaianum CCALA960, isolates AP17 and AP24 should be considered as a second novel species in the Oxynema genus, for which the name Oxynema aestuarii sp. nov. is proposed.

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Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02975-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 2223-2230 ◽

Cited By ~ 105

Author(s):

Linxian Ding ◽

Akira Yokota

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Phylogenetic Study ◽

Well Water ◽

Rrna Gene ◽

Bacterial Strains ◽

Gram Negative ◽

Morphological Studies ◽

The 16S Rrna Gene

Two strains of curved bacteria, 7-1T and 7-2T, isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1T is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1T formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA–DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1T, [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1T (=IAM 15033T=ATCC BAA-807T) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2T is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2T (=IAM 15032T=ATCC BAA-806T) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.

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Identification and phylogenetic study of bioluminescent bacteria from squid (Loligo duvaucelii) based on 16S rRNA gene

10.1063/1.5050134 ◽

2018 ◽

Author(s):

Melati Putri Pertiwi ◽

Patricia Karin Himawan Praseptin ◽

Ika Diana Werdani ◽

Dwi Listyorini ◽

Sitoresmi Prabaningtyas

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Study ◽

Rrna Gene ◽

Bioluminescent Bacteria

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Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63534-0 ◽

2005 ◽

Vol 55 (4) ◽

pp. 1439-1452 ◽

Cited By ~ 63

Author(s):

Endalkachew Wolde-meskel ◽

Zewdu Terefework ◽

Åsa Frostegård ◽

Kristina Lindström

Keyword(s):

Genetic Diversity ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Genes ◽

Partial Sequence ◽

23S Rrna ◽

Southern Ethiopia ◽

Rrna Gene ◽

Pcr Rflp ◽

23S Rrna Gene

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

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Evidence that Bacteroides nodosus Belongs in Subgroup Gamma of the Class Proteobacteria, Not in the Genus Bacteroides: Partial Sequence Analysis of a B. nodosus 16S rRNA Gene

International Journal of Systematic Bacteriology ◽

10.1099/00207713-40-2-154 ◽

1990 ◽

Vol 40 (2) ◽

pp. 154-159 ◽

Cited By ~ 9

Author(s):

S. LA FONTAINE ◽

J. I. ROOD

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Partial Sequence ◽

Rrna Gene

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Molecular investigations of the stalked barnacleVulcanolepas osheaiand the epibiotic bacteria from the Brothers Caldera, Kermadec Arc, New Zealand

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315409000459 ◽

2009 ◽

Vol 89 (4) ◽

pp. 727-733 ◽

Cited By ~ 18

Author(s):

Yohey Suzuki ◽

Masae Suzuki ◽

Shinji Tsuchida ◽

Ken Takai ◽

Koki Horikoshi ◽

...

Keyword(s):

Fatty Acids ◽

New Zealand ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Filamentous Bacteria ◽

Carbon Isotopic ◽

Phylogenetic Affiliation ◽

Isotopic Analyses ◽

Molecular Phylogenetic

The hydrothermal-vent barnacleVulcanolepas osheaiof the subfamily Neolepadinae is one of the most conspicuous organisms at the Brothers Caldera, south Kermadec Arc, New Zealand. Like a neolepad species found in the Lau Basin,V. osheaiharbours filamentous bacteria on its elongated cirral setae. To define the phylogenetic affiliation of the epibiotic bacteria and the nutrition of the barnacle host, we conducted molecular phylogenetic and isotopic analyses. Analysis of 16S rRNA gene sequences of microbial communities on the cirral setae showed that among 91 bacterial sequences investigated, 28 sequences were related to the ɛ-proteobacterial endosymbiont ofAlviniconchaaff.hessleri; 11 sequences were related to the epibiont of the bresiliid shrimpRimicarisexoculata. Fluorescencein situhybridization showed that in contrary to results from the 16S rRNA gene-sequence library, approximately 80% of the filamentous bacteria hybridized with a probe targeting the sequences related to the epibiont of the bresiliid shrimpR. exoculata. The fatty-acid profiles of the filamentous bacteria and the host barnacle both contained high levels of monounsaturated C16and C18fatty acids, and the carbon isotopic compositions of the biomass and monounsaturated C16and C18fatty acids of both the bacteria and barnacle were nearly identical. This would suggest that the nutrition of the barnacle is highly dependent on bacteria thriving around the barnacle, including the epibiotic bacteria.

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Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63201-0 ◽

2005 ◽

Vol 55 (5) ◽

pp. 1965-1972 ◽

Cited By ~ 92

Author(s):

Rinku Pal ◽

Shashi Bala ◽

Mandeep Dadhwal ◽

Mukesh Kumar ◽

Gauri Dhingra ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Study ◽

Rrna Gene ◽

Sphingomonas Paucimobilis ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Dna Relatedness ◽

Sphingobium Chlorophenolicum ◽

Sphingomonas Xenophaga

Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837T, but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152T followed by Sphingobium chlorophenolicum ATCC 33790T. The three strains showed low DNA–DNA relatedness values with Sphingomonas paucimobilis ATCC 29837T (8–25 %), [Sphingomonas] chungbukensis IMSNU 11152T (10–17 %), Sphingobium chlorophenolicum ATCC 33790T (23–54 %) and Sphingomonas xenophaga DSM 6383T (10–28 %), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99·1–99·4 %), DNA–DNA relatedness (19–59 %) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152T formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364T=CCM 7286T), Sphingobium japonicum sp. nov. (=MTCC 6362T=CCM 7287T) and Sphingobium francense sp. nov. (=MTCC 6363T=CCM 7288T), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.

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