scholarly journals Molecular Diversity of New Thermococcales Isolates from a Single Area of Hydrothermal Deep-Sea Vents as Revealed by Randomly Amplified Polymorphic DNA Fingerprinting and 16S rRNA Gene Sequence Analysis

2004 ◽  
Vol 70 (3) ◽  
pp. 1277-1286 ◽  
Author(s):  
Elodie Lepage ◽  
Evelyne Marguet ◽  
Claire Geslin ◽  
Oriane Matte-Tailliez ◽  
Wolfram Zillig ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Model Organisms ◽  
Rrna Gene ◽  
Randomly Amplified Polymorphic Dna ◽  
Hot Environments ◽  
High Degree ◽  
Reference Strains

ABSTRACT Members of the Thermococcales are anaerobic Archaea belonging to the kingdom Euryarchaea that are studied in many laboratories as model organisms for hyperthermophiles. We describe here a molecular analysis of 86 new Thermococcales isolates collected from six different chimneys of a single hydrothermal field located in the 13�N 104�W segment of the East Pacific ridge at a depth of 2,330 m. These isolates were sorted by randomly amplified polymorphic DNA (RAPD) fingerprinting into nine groups, and nine unique RAPD profiles were obtained. One RAPD group corresponds to new isolates of Thermococcus hydrothermalis, whereas all other groups and isolates with unique profiles are different from the 22 reference strains included in this study. Analysis of 16S rRNA gene sequences of representatives of each RAPD group and unique profiles showed that one group corresponds to Pyrococcus strains, whereas all the other isolates are Thermococcus strains. We estimated that our collection may contain at least 11 new species. These putative species, isolated from a single area of hydrothermal deep-sea vents, are dispersed in the 16S rRNA tree among the reference strains previously isolated from diverse hot environments (terrestrial, shallow water, hydrothermal vents) located around the world, suggesting that there is a high degree of dispersal of Thermococcales. About one-half of our isolates contain extrachromosomal elements that could be used to search for novel replication proteins and to develop genetic tools for hyperthermophiles.

scholarly journals Pseudomonas knackmussii sp. nov.

2007 ◽  
Vol 57 (3) ◽  
pp. 572-576 ◽  
Author(s):  
Andreas Stolz ◽  
Hans-Jürgen Busse ◽  
Peter Kämpfer
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Fatty Acid Profile ◽  
Rrna Gene ◽  
Pseudomonas Nitroreducens ◽  
High Degree ◽  
Reference Strains ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

The taxonomic position of Pseudomonas sp. B13T, isolated as a 3-chlorobenzoate-degrading organism and used for several groundbreaking studies on the enzymology and genetics of the degradative pathway for haloaromatic compounds, was studied in detail. The previously performed physiological studies, the detection of ubiquinone Q-9, the polyamine pattern with putrescine and spermidine as major polyamines, a fatty acid profile with C18 : 1 ω7c, summed feature 3 and C16 : 0 as quantitatively the most important constituents and the 16S rRNA gene sequence demonstrated that Pseudomonas sp. B13T indeed belongs to the genus Pseudomonas. The sequence of the Pseudomonas sp. B13T 16S rRNA gene demonstrated a high degree of similarity with that of Pseudomonas citronellolis DSM 50332T (98.9 %), Pseudomonas nitroreducens DSM 14399T (98.7 %), Pseudomonas jinjuensis DSM 16612T (98.1 %) and Pseudomonas multiresinivorans DSM 17553T (98.7 %). Thus it was shown that strain Pseudomonas sp. B13T can be distinguished from related species by the ability/inability to assimilate N-acetylgalactosamine, d-galactose, putrescine, trans-aconitate and mesaconate and some differences in the fatty acid profile. The positioning of Pseudomonas sp. B13T as a separate taxon was finally verified by DNA hybridization, which demonstrated less than 45 % DNA–DNA similarity between strain Pseudomonas sp. B13T and the reference strains. On the basis of these results, Pseudomonas sp. B13T represents a novel species for which the name Pseudomonas knackmussii sp. nov. is proposed. The type strain is B13T (=DSM 6978T=LMG 23759T).

scholarly journals Molecular Detection of Some Anaplasma Species in Blood of Dogs in Baghdad Province, Iraq

2020 ◽  
Vol 44 (1) ◽  
pp. 39-45 ◽  
Author(s):  
Suha S. Ahmed Al –Obaidi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Nucleotide Sequencing ◽  
Rrna Gene ◽  
16S Rna ◽  
Pcr Products ◽  
Polymerase Chain ◽  
High Degree ◽  
Reference Strains ◽  
Canine Anaplasmosis

A total of 150 blood samples were collected from dogs and examined by the polymerase chain reaction (PCR) technique, which was used to detect the 16S RNA gene of Anaplasma platys and Anaplasma phagocytophilum. Subsequent analysis of the PCR amplicons was achieved by nucleotides sequencing of some positive samples. Totally, the findings show the presence of PCR products (i.e. Anaplasma spp. infection) in 12/150 (8.0%) of the dogs under study. While 5/150 (3.33%) of the cases were A. platys, 7/150 (4.66%) were A. phagocytophilum. Nucleotide sequencing confirmed the identity of the amplified genes whose sequences were compared with other references belong to 15 of 16S rRNA gene of A platys and 14 references of 16S rRNA gene of A. phagocytophilum, and the sequences of this study isolates were deposited on the Gene Bank. The identity and similarity scores between the isolates of this study and reference strains ranged from 98 to 99%. In conclusion, canine anaplasmosis prevalence in dogs could be underestimated in Iraq, and the phylogenetic tree of the local A. platys and A. phagocytophilum isolates were found to resemble other worldwide strains of Anaplasma spp. with a high degree of similarity.

scholarly journals Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield

2007 ◽  
Vol 57 (2) ◽  
pp. 250-254 ◽  
Author(s):  
Jun Gu ◽  
Hua Cai ◽  
Su-Lin Yu ◽  
Ri Qu ◽  
Bin Yin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Saline Soil ◽  
Sequence Similarity ◽  
Eastern China ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Shengli Oilfield ◽  
Major Respiratory Quinone ◽  
Reference Strains

Two novel strains, SL014B61AT and SL014B11A, were isolated from an oil-polluted saline soil from Gudao in the coastal Shengli Oilfield, eastern China. Cells of strains SL014B61AT and SL014B11A were motile, Gram-negative and rod-shaped. Growth occurred at NaCl concentrations of between 0 and 15 % and at temperatures of between 10 and 45 °C. Strain SL014B61AT had Q9 as the major respiratory quinone and C16 : 0 (21.2 %), C18 : 1ω9c (20.3 %), C16 : 1ω7c (7.3 %) and C16 : 1ω9c (6.4 %) as predominant fatty acids. The G+C content of the DNA was 57.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SL014B61AT belonged to the genus Marinobacter in the class Gammaproteobacteria. Strain SL014B61AT showed the highest 16S rRNA gene sequence similarity with Marinobacter bryozoorum (97.9 %) and showed 97.8 % sequence similarity to Marinobacter lipolyticus. DNA–DNA relatedness to the reference strains Marinobacter bryozoorum and Marinobacter lipolyticus was 35.5 % and 33.8 %, respectively. On the basis of these data, it is proposed that strains SL014B61AT and SL014B11A represent a novel species, Marinobacter gudaonensis sp. nov. The type strain is strain SL014B61AT (=DSM 18066T=LMG 23509T=CGMCC 1.6294T).

scholarly journals Amplification of 16S rRNA gene sequences to differentiate two highly related bradyrhizobia species

2007 ◽  
Vol 42 (9) ◽  
pp. 1361-1364 ◽  
Author(s):  
Adriana Giongo ◽  
Adriana Ambrosini ◽  
João Ruy Jardim Freire ◽  
Maria Helena Bodanese Zanettini ◽  
Luciane Maria Pereira Passaglia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bradyrhizobium Japonicum ◽  
Diagnostic Method ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Reference Strains ◽  
Commercial Inoculants

A 16S rRNA gene PCR-based assay was developed aiming at a fast molecular diagnostic method to differentiate the two phylogenetically closely related species Bradyrhizobium japonicum and B. elkanii, isolated from soybean nodules, in order to identify those more competitive and comprising greater nitrogen fixation ability for use in the formulation of commercial inoculants. The assay used was able to discriminate ten reference strains belonging to these two Bradyrhizobium species, as well as to efficiently identify 37 strains isolated from fields cultivated with soybean.

scholarly journals Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

2018 ◽  
Author(s):  
Karen G. Lloyd ◽  
Joshua Ladau ◽  
Andrew D. Steen ◽  
Junqi Yin ◽  
Lonnie Crosby
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrothermal Vents ◽  
Hot Springs ◽  
Laboratory Culture ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Microbial Cells ◽  
Taxonomic Groups

AbstractTo unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029(81%) and 2.2 × 1029(25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

scholarly journals Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods

2001 ◽  
Vol 67 (7) ◽  
pp. 3077-3085 ◽  
Author(s):  
Wolfgang Eder ◽  
Linda L. Jahnke ◽  
Mark Schmidt ◽  
Robert Huber
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Deep Sea ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Cultivation Methods

ABSTRACT The brine-seawater interface of the Kebrit Deep, northern Red Sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. Under strictly anaerobic culture conditions, novel halophiles were isolated. The new rod-shaped isolates belong to the halophilic genus Halanaerobiumand are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. Within the genus Halanaerobium, they represent new species which grow chemoorganotrophically at NaCl concentrations ranging from 5 to 34%. The cellular fatty acid compositions are consistent with those of otherHalanaerobium representatives, showing unusually large amounts of Δ7 and Δ11 16:1 fatty acids. Phylogenetic analysis of the brine-seawater interface sample revealed the presence of various bacterial 16S rRNA gene sequences dominated by cultivated members of the bacterial domain, with the majority affiliated with the genusHalanaerobium. The new Halanaerobium 16S rRNA clone sequences showed the highest similarity (99.9%) to the sequence of isolate KT-8-13 from the Kebrit Deep brine. In this initial survey, our polyphasic approach demonstrates that novel halophiles thrive in the anaerobic, deep-sea brine pool of the Kebrit Deep, Red Sea. They may contribute significantly to the anaerobic degradation of organic matter enriched at the brine-seawater interface.

scholarly journals Resuscitation of eleven-year VBNC Citrobacter

2008 ◽  
Vol 6 (4) ◽  
pp. 565-568 ◽  
Author(s):  
Amel Dhiaf ◽  
Amina Bakhrouf ◽  
Karl-Paul Witzel
Keyword(s):  
Growth Factors ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Strain ◽  
Rrna Gene ◽  
Citrobacter Freundii ◽  
16S Rrna Gene Sequences ◽  
High Degree ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

Citrobacter freundii strain WA1 was stressed by incubation in seawater microcosms for eleven years. After two years of starvation, no culturable strain was observed. Incubation of samples in nutrient-rich broth medium not supplemented with growth factors, however, allowed resuscitation of VBNC cells so that subsequent plating yielded observable colonies for significantly extended periods of time. Recovery of VBNC Citrobacter freundii was obtained by incubation in nutrient broth even after eleven years of starvation. To see whether the samples contained the same strain of Citrobacter freundii inoculated 11 years ago. The complete 16S rRNA gene was PCR amplified and sequenced from initial, stressed and revived strains of Citrobacter freundii strain WA1.The 16S rRNA gene sequences from eleven-year stressed strains were homologous with a high degree of similarity to the GenBank reference strain and were identical to each other.

scholarly journals Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

2004 ◽  
Vol 54 (5) ◽  
pp. 1543-1551 ◽  
Author(s):  
C. Y. Turenne ◽  
V. J. Cook ◽  
T. V. Burdz ◽  
R. J. Pauls ◽  
L. Thibert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Great Part ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Culture Collections ◽  
Clinical Specimens ◽  
Mycobacterium Simiae ◽  
Reference Strains

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).

Luteimonas abyssi sp. nov., isolated from deep-sea sediment

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 668-674 ◽  
Author(s):  
Xiaoyang Fan ◽  
Tong Yu ◽  
Zhao Li ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031T, XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51′ S 153° 6′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9T (96.95 %), Luteimonas huabeiensis HB2T (96.93 %) and Xanthomonas cucurbitae LMG 690T (96.92 %). The DNA G+C contents of the three isolates were 70.2–73.9 mol%. The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C11 : 0 and C16 : 010-methyl and/or iso-C17 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas , for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031T ( = DSM 25880T = CGMCC 1.12611T).

Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 251-259 ◽  
Author(s):  
Patricia L. Tavormina ◽  
Roland Hatzenpichler ◽  
Shawn McGlynn ◽  
Grayson Chadwick ◽  
Katherine S. Dawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sequence Identity ◽  
Link Type

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1T, ‘whale fall 1’) that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina . Strain WF1T represents the first cultivar from the ‘deep sea-1’ clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1T were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1T was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1T, a capacity that had not been functionally demonstrated previously in members of Methylobacter . On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1T ( = LMG 28393T = ATCC BAA-2619T).

Sign in / Sign up

Export Citation Format

Share Document