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 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 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 Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The 16S Rrna Gene

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).

scholarly journals Polaribacter dokdonensis sp. nov., isolated from seawater

2006 ◽  
Vol 56 (6) ◽  
pp. 1251-1255 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

scholarly journals Algoriphagus terrigena sp. nov., isolated from soil

2006 ◽  
Vol 56 (4) ◽  
pp. 777-780 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming bacterial strain, DS-44T, was isolated from soil from Dokdo in Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and in the presence of 2 % (w/v) NaCl. Strain DS-44T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 49·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-44T belongs to the genus Algoriphagus of the phylum Bacteroidetes. Similarity values between the 16S rRNA gene sequences of strain DS-44T and those of the type strains of recognized Algoriphagus species were in the range 93·8–95·7 %, making it possible to categorize strain DS-44T as a species that is separate from previously described Algoriphagus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-44T (=KCTC 12545T=CIP 108837T) was classified in the genus Algoriphagus as the type strain of a novel species, for which the name Algoriphagus terrigena sp. nov. is proposed.

scholarly journals EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2259-2261 ◽  
Author(s):  
Jongsik Chun ◽  
Jae-Hak Lee ◽  
Yoonyoung Jung ◽  
Myungjin Kim ◽  
Seil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Multiple Sequence ◽  
Web Based ◽  
Routine Identification ◽  
Type Strains

16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates. The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/

scholarly journals Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo

2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Two Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.

scholarly journals Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum

2007 ◽  
Vol 57 (10) ◽  
pp. 2284-2288 ◽  
Author(s):  
Seo-Youn Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains

Two Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1 ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).

scholarly journals Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater

2010 ◽  
Vol 60 (6) ◽  
pp. 1413-1417 ◽  
Author(s):  
Young Sun Lee ◽  
Dong-Heon Lee ◽  
Hyung-Yeel Kahng ◽  
Eun Mi Kim ◽  
Jae Sung Jung
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Erythrobacter Litoralis ◽  
Ubiquinone 10 ◽  
Distinct Phylogenetic Lineage ◽  
Type Strains

A novel Gram-negative, aerobic, orange-pigmented bacterial strain, designated K7-2T, was isolated from seawater of Gangjin Bay, Korea, and subjected to a polyphasic taxonomic study. Strain K7-2T contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and did not produce bacteriochlorophyll a. Major fatty acids were C18 : 1 ω7c (51.4 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (15.0 %) and C17 : 1 ω6c (8.8 %). Major polar lipids were phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content was 61.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain K7-2T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Similarities between the 16S rRNA gene sequences of strain K7-2T and the type strains of Erythrobacter species ranged from 95.0 % (Erythrobacter litoralis DSM 8509T) to 96.8 % (Erythrobacter citreus RE35F/1T). On the basis of polyphasic taxonomic data, strain K7-2T (=KCTC 22330T=JCM 15420T) is classified in a novel species within the genus Erythrobacter, for which the name Erythrobacter gangjinensis sp. nov. is proposed.

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