scholarly journals Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009

2011 ◽  
Vol 61 (6) ◽  
pp. 1259-1264 ◽  
Author(s):  
D. P. Labeda ◽  
M. Goodfellow ◽  
J. Chun ◽  
X.-Y. Zhi ◽  
W.-J. Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

The taxonomic status of the families Actinosynnemataceae and Pseudonocardiaceae was assessed based on 16S rRNA gene sequence data available for the 151 taxa with validly published names, as well as chemotaxonomic and morphological properties available from the literature. 16S rRNA gene sequences for the type strains of all taxa within the suborder Pseudonocardineae were subjected to phylogenetic analyses using different algorithms in arb and phylip. The description of many new genera and species within the suborder Pseudonocardineae since the family Actinosynnemataceae was proposed in 2000 has resulted in a markedly different distribution of chemotaxonomic markers within the suborder from that observed at that time. For instance, it is noted that species of the genera Actinokineospora and Allokutzneria contain arabinose in whole-cell hydrolysates, which is not observed in the other genera within the Actinosynnemataceae, and that there are many genera within the family Pseudonocardiaceae as currently described that do not contain arabinose. Phylogenetic analyses of 16S rRNA gene sequences for all taxa within the suborder do not provide any statistical support for the family Actinosynnemataceae, nor are signature nucleotides found that support its continued differentiation from the family Pseudonocardiaceae. The description of the family Pseudonocardiaceae is therefore emended to include the genera previously classified within the family Actinosynnemataceae and the description of the suborder Pseudonocardineae is also emended to reflect this reclassification.

scholarly journals Evolution of Thermotolerance in Hot Spring Cyanobacteria of the Genus Synechococcus

2000 ◽  
Vol 66 (10) ◽  
pp. 4222-4229 ◽  
Author(s):  
Scott R. Miller ◽  
Richard W. Castenholz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hot Spring ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Ecological Diversification ◽  
Physiological Approach

ABSTRACT The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.

scholarly journals Pedobacter sandarakinus sp. nov., isolated from soil

2006 ◽  
Vol 56 (6) ◽  
pp. 1273-1277 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Soo-Yeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Family ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, rod-shaped bacterial strain, designated DS-27T, was isolated from a soil sample, and its taxonomic position was investigated by using a polyphasic approach. The organism grew optimally at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Strain DS-27T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-27T is most closely related to the genus Pedobacter of the family Sphingobacteriaceae. Similarity values between the 16S rRNA gene sequences of strain DS-27T and the type strains of recognized Pedobacter species ranged from 90.6 to 95.5 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to categorize strain DS-27T as representing a species that is separate from recognized Pedobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-27T (=KCTC 12559T=CIP 108922T) was classified in the genus Pedobacter as a member of a novel species, for which the name Pedobacter sandarakinus sp. nov. is proposed.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2289-2295 ◽  
Author(s):  
Madalin Enache ◽  
Takashi Itoh ◽  
Tadamasa Fukushima ◽  
Ron Usami ◽  
Lucia Dumitru ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Marker ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Rpob Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.

scholarly journals Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 723-731 ◽  
Author(s):  
Ronel Roberts ◽  
Emma T. Steenkamp ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nucleotide Sequence Data ◽  
Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

Sphingobium fontiphilum sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1906-1911 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were Sphingobium amiense YTT, Sphingobium yanoikuyae GIFU 9882T and Sphingobium scionense WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus Sphingobium . The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus Sphingobium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus Sphingobium , for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).

scholarly journals Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983

2006 ◽  
Vol 56 (8) ◽  
pp. 1721-1724 ◽  
Author(s):  
Franco Dellaglio ◽  
Marc Vancanneyt ◽  
Akihito Endo ◽  
Peter Vandamme ◽  
Giovanna E. Felis ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Dna ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Characteristics ◽  
Binding Level

The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.

scholarly journals Poritiphilus flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coral Porites lutea

2020 ◽  
Vol 70 (11) ◽  
pp. 5620-5626 ◽  
Author(s):  
Guanghua Wang ◽  
Shuailiang Xu ◽  
Ge Dang ◽  
Jianfeng Liu ◽  
Hongfei Su ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Porites Lutea ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, non-endospore-forming, non-motile, aerobic bacterium (strain R33T) was isolated from coral Porites lutea and subjected to a polyphasic taxonomic study. The G+C content was 44.5 mol%. The only detected respiratory quinone was menaquinone 6 (MK-6). The major cellular fatty acids were iso-C15 : 0 and iso-C15 : 1 ω6c. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Global alignment based on 16S rRNA gene sequences indicated that strain R33T shares the highest sequence identity of 93.2 % with Muriicola marianensis A6B8T in the family Flavobacteriaceae . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R33T forms a distinct branch in a stable clade comprising strain R33T and members of the genera Muriicola , Robiginitalea , Eudoraea and Zeaxanthinibacter . The phylogenomic analysis also supported this 16S rRNA gene-based phylogenetic result. Comparative genomic analysis indicated that strain R33T is rich in AraC-type DNA-binding domain-containing protein-coding genes, which means the regulation of carbon utilization is very complex. Low 16S rRNA gene identity, different polar lipids and/or cellular fatty acid profiles could readily distinguish strain R33T from any validly published type strains. Therefore, strain R33T is suggested to represent a new species in a new genus, for which the name Poritiphilus flavus gen. nov., sp. nov. is proposed. The type strain is R33T (=MCCC 1K03853T=KCTC 72443T).

Description of a novel coccoid cyanobacterial genus and species Sinocapsa zengkensis gen. nov. sp. nov. (Sinocapsaceae, incertae sedis), with taxonomic notes on genera in Chroococcidiopsidales

Phytotaxa ◽  
2019 ◽  
Vol 409 (3) ◽  
pp. 146-160 ◽  
Author(s):  
YILANG WANG ◽  
FANGFANG CAI ◽  
NANNAN JIA ◽  
RENHUI LI
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Concrete Surface ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Incertae Sedis ◽  
Molecular Features ◽  
The Family

A new terrestrial coccoid cyanobacterial strain was isolated in depression of a rough concrete surface in village Zengkeng, Fujian Province, China. This strain, named CHAB 6571, was characterized by a polyphasic approach. The strain exhibited morphological similarity to the Aliterlella species but differed in its larger cell sizes and irregular arranged thylakoids. 16S rRNA gene sequences of the strain had the maximum homology as 94.13 % to the genus Aliterella. The phylogeny based on 16S rRNA gene sequences revealed that there were four separated coccoid cyanobacterial clusters formed in the position representing Chroococcidiopsidales, at the vicinity of Nostocales and away from other coccoid cyanobacterial orders such as Chroococcales, Pleurocapsales and Synechococcales. These four main clusters as the CHAB 6571 in cluster A, genus Aliterella of the family Aliterellaceae in cluster B, Chroococcidiopsis sensu stricto of Chroococcidiopsidaceae in cluster C, and genera Chroogloeocystis and Gloeocapsopsis in cluster D, were likely to represent four different families with their 16S rRNA gene sequences similarities as 90–94%. However, the 16S rRNA phylogenetic results also revealed that the Chroococcidiopsidales were not monophyletic since the organisms belonging to Oscillatoriales such as Cephalothrix, Aerosakkonema and Microseira were phylogenetically mixed into the Chroococcidiopsidales. Combining the morphological, ecological and molecular features, CHAB 6571 as a new genus and species, as well as a novel family were therefore established, named Sinocapsa zengkensis (Sinocapsaceae, incertae sedis).

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