scholarly journals Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-‘Synechococcus’ clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon The GenBank accession numbers for the ITS amplicon sequences reported in this paper are AF387607 (PCC 9511T), AF387610 (PCC 6307), AF387608 (PCC 7001) and AF387609 (PCC 7941).

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 453-465 ◽  
Author(s):  
Wassila Laloui ◽  
Katarzyna A Palinska ◽  
Rosmarie Rippka ◽  
Frédéric Partensky ◽  
Nicole Tandeau de Marsac ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Low Light ◽  
Dna Base Composition ◽  
Dna Base ◽  
Ribosomal Operon ◽  
Group Specific Primer

PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of ‘Synechococcus’ (WH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511T, although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 16S rRNA gene sequences. The ITSs of three strains (PCC 9511T, PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-‘Synechococcus’ strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted clade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.

scholarly journals Asaia krungthepensis sp. nov., an acetic acid bacterium in the α-Proteobacteria

2004 ◽  
Vol 54 (2) ◽  
pp. 313-316 ◽  
Author(s):  
Pattaraporn Yukphan ◽  
Wanchern Potacharoen ◽  
Somboon Tanasupawat ◽  
Morakot Tanticharoen ◽  
Yuzo Yamada
Keyword(s):  
Acetic Acid ◽  
Enrichment Culture ◽  
Acetic Acid Bacteria ◽  
Acetic Acid Bacterium ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Dna Base Composition ◽  
Dna Base ◽  
Type Strains

Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60·2–60·5 mol% G+C, with a range of 0·3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA–DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q10. On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08T (=BCC 12978T=TISTR 1524T=NBRC 100057T=NRIC 0535T), which had a DNA G+C content of 60·3 mol% and was isolated from a heliconia flower (‘paksaasawan’ in Thai; Heliconia sp.) collected in Bangkok, Thailand.

scholarly journals Distribution and recombination of Wolbachia endosymbionts in Korean coleopteran insects

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Gilsang Jeong ◽  
Taeman Han ◽  
Haechul Park ◽  
Soyeon Park ◽  
Pureum Noh
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Surface Protein ◽  
Rrna Gene ◽  
Infection Frequency ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Endosymbiotic Bacteria ◽  
Molecular Machinery ◽  
Broad Scale

Abstract Background Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

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 Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

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.

scholarly journals Marichromatium fluminis sp. nov., a slightly alkaliphilic, phototrophic gammaproteobacterium isolated from river sediment

2010 ◽  
Vol 60 (5) ◽  
pp. 1103-1107 ◽  
Author(s):  
K. Sucharita ◽  
E. Shiva Kumar ◽  
Ch. Sasikala ◽  
B. B. Panda ◽  
S. Takaichi ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Base Composition ◽  
Dna Base ◽  
Gene Sequence Analysis

An anoxygenic, phototrophic gammaproteobacterium designated strain JA418T was isolated from a sediment sample collected from the Baitarani River, Orissa, India. The bacterium was a Gram-negative, motile rod with a single polar flagellum. Bacteriochlorophyll a and rhodopin were the major photosynthetic pigments. The organism grew best at slightly alkaline pH (8–8.5) and lacked chemotrophic growth. The major fatty acids were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA418T clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest 16S rRNA gene sequence similarities of strain JA418T were found with the type strains of Marichromatium gracile (95.9 %), Marichromatium indicum (95.6 %), Marichromatium purpuratum (95.5 %) and Marichromatium bheemlicum (95.6 %). The DNA base composition of strain JA418T was 71.4 mol% G+C (by HPLC). Based on the 16S rRNA gene sequence analysis and physiological and chemotaxonomic characteristics, strain JA418T is sufficiently different from other Marichromatium species to merit the description of a novel species, Marichromatium fluminis sp. nov., to accommodate it. The type strain is JA418T (=KCTC 5717T =NBRC 105221T).

scholarly journals Jonesia quinghaiensis sp. nov., a new member of the suborder Micrococcineae

2004 ◽  
Vol 54 (6) ◽  
pp. 2181-2184 ◽  
Author(s):  
Peter Schumann ◽  
Xiaolong Cui ◽  
Erko Stackebrandt ◽  
Reiner M. Kroppenstedt ◽  
Lihua Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Soda Lake ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Dna Base Composition ◽  
Dna Base

A coryneform strain isolated from soda lake mud in China corresponded in chemotaxonomic characteristics such as peptidoglycan type A4α l-lys–l-ser–d-Glu and major menaquinone MK-9, as well as in its DNA base composition (57 mol% G+C), to its phylogenetic neighbour Jonesia denitrificans. Differences in phenotypic characteristics and the phylogenetic distance (96·6 % 16S rRNA gene sequence similarity) from J. denitrificans justify the proposal of a second species of the genus Jonesia, Jonesia quinghaiensis sp. nov., with the type strain QH3A7T (=DSM 15701T=CGMCC 1.3459T).

scholarly journals Identification of Medically RelevantTrichosporon Species Based on Sequences of Internal Transcribed Spacer Regions and Construction of a Database forTrichosporon Identification

1999 ◽  
Vol 37 (6) ◽  
pp. 1985-1993 ◽  
Author(s):  
Takashi Sugita ◽  
Akemi Nishikawa ◽  
Reiko Ikeda ◽  
Takako Shinoda
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Comparative Sequence Analysis ◽  
Nucleotide Sequences ◽  
Its Sequences ◽  
Rrna Gene ◽  
Comparative Sequence ◽  
Internal Transcribed Spacer Regions ◽  
Molecular Phylogenetic

The nucleotide sequences of the internal transcribed spacer (ITS) 1 and 2 regions in the rRNA gene were determined by directly sequencing PCR-amplified fragments for all of the species (17 species and five varieties) in the genus Trichosporon. Comparative sequence analysis suggests that six medically relevant species, T. asahii, T. asteroides, T. cutaneum,T. inkin, T. mucoides, and T. ovoides, can be readily identified by their ITS sequences. In addition, the sequence analysis showed that conspecific strains have fewer than 1% nucleotide differences in the ITS 1 and 2 regions overall. Molecular phylogenetic trees are also presented.

scholarly journals Phylogenetic Relationships of Yessotoxin-Producing Dinoflagellates, Based on the Large Subunit and Internal Transcribed Spacer Ribosomal DNA Domains

2008 ◽  
Vol 75 (1) ◽  
pp. 54-63 ◽  
Author(s):  
Meredith D. A. Howard ◽  
G. Jason Smith ◽  
Raphael M. Kudela
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Rrna Gene ◽  
Multiple Sequence ◽  
Lingulodinium Polyedrum ◽  
Marine Toxin ◽  
Ribosomal Operon ◽  
Toxic Blooms ◽  
Genomic Regions

ABSTRACT Yessotoxin (YTX) is a globally distributed marine toxin produced by some isolates of the dinoflagellate species Protoceratium reticulatum, Lingulodinium polyedrum, and Gonyaulax spinifera within the order Gonyaulacales. The process of isolating cells and testing each isolate individually for YTX production during toxic blooms are labor intensive, and this impedes our ability to respond quickly to toxic blooms. In this study, we used molecular sequences from the large subunit and internal transcribed spacer genomic regions in the ribosomal operon of known YTX-producing dinoflagellates to determine if genetic differences exist among geographically distinct populations or between toxic and nontoxic isolates within species. In all analyses, all three YTX-producing species fell within the Gonyaulacales order in agreement with morphological taxonomy. Phylogenetic analyses of available rRNA gene sequences indicate that the capacity for YTX production appears to be confined to the order Gonyaulacales. These findings indicate that Gonyaulacoloid dinoflagellate species are the most likely to produce YTX and thus should be prioritized for YTX screening during events. Dinoflagellate species that fall outside of the Gonyaulacales order are unlikely to produce YTX. Although the rRNA operon offers multiple sequence domains to resolve species level diversification within this dinoflagellate order, these domains are not sufficiently variable to provide robust markers for YTX toxicity.

scholarly journals “Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria

2013 ◽  
Vol 79 (10) ◽  
pp. 3241-3248 ◽  
Author(s):  
Matteo Montagna ◽  
Davide Sassera ◽  
Sara Epis ◽  
Chiara Bazzocchi ◽  
Claudia Vannini ◽  
...  
Keyword(s):  
Life History ◽  
16S Rrna ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Evolutionary Scenario ◽  
Wide Range ◽  
Midichloria Mitochondrii

ABSTRACT“CandidatusMidichloria mitochondrii” is an intramitochondrial bacterium of the orderRickettsialesassociated with the sheep tickIxodes ricinus. Bacteria phylogenetically related to “Ca. Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of theRickettsiales. This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent novel genera; (iii) the MALO group ranks at the level of describedRickettsialesfamilies, leading to the proposal of the novel family “CandidatusMidichloriaceae.” In addition, based on the phylogenetic trees generated, we present an evolutionary scenario to interpret the distribution and life history transitions of these microorganisms associated with highly divergent eukaryotic hosts: we suggest that aquatic/environmental protista have acted as evolutionary reservoirs for members of this novel family, from which one or more lineages with the capacity of infecting metazoa have evolved.

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