Kribbella deserti sp. nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus.

PubMed

Sun, Ji-Quan; Xu, Lian; Guo, Yan; Li, Wei-Le; Shao, Zhong-Qiu; Yang, Yuan-Liang; Wu, Xiao-Lei

2017-03-01

A Gram-stain-positive, aerobic bacterial strain, designated SL15-1 T , was isolated from desert soil which was sampled from the rhizosphere of Ammopiptanthus mongolicus, Hangjin Banner, Ordos, Inner Mongolia, northern China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SL15-1 T was clustered with Kribbella strains, sharing the highest similarity of 16S rRNA gene sequence (96.97 %) with Kribbella sandramycini DSM 15626 T . Strain SL15-1 T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown phospholipid, an unknown lipid and two unknown aminophospholipids as the major polar lipids. MK-9(H4) was the predominant menaquinone, while anteiso-C15 : 0, iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 65.3 mol%. The results of physiological and biochemical tests allowed the discrimination of strain SL15-1 T from its phylogenetic relatives. Kribbella deserti sp. nov. is therefore proposed with strain SL15-1 T (=CGMCC 1.15906 T =KCTC 39825 T ) as the type strain.

Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community.

PubMed

Patel, Nisha B; Tito, Raul Y; Obregón-Tito, Alexandra J; O'Neal, Lindsey; Trujillo-Villaroel, Omar; Marin-Reyes, Luis; Troncoso-Corzo, Luzmila; Guija-Poma, Emilio; Lewis, Cecil M; Lawson, Paul A

2016-05-01

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).

Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle.

PubMed

Lee, Geun-Hye; Rhee, Moon-Soo; Chang, Dong-Ho; Lee, Jonghwan; Kim, Seil; Yoon, Min Ho; Kim, Byoung-Chan

2013-06-01

A strictly anaerobic, Gram-negative, non-spore-forming bacterium, designated GH1(T), was isolated from the rumen of Korean native cattle (HanWoo). Cells were straight to slightly curved rods (2.0-4.5 µm long) and were motile by peritrichous flagella. The isolate grew at 30-45 °C (optimum 40 °C), at pH 5.5-6.5 (optimum pH 6.0) and with up to 3.5% (w/v) NaCl. Strain GH1(T) produced acid from d-glucose, d-ribose and d-xylose, with butyric acid being the major end product. The genomic DNA G+C content was 54.6 mol%. Based on comparative 16S rRNA gene sequence analysis, strain GH1(T) was most closely related to Oscillibacter valericigenes Sjm18-20(T) (97.3% 16S rRNA gene sequence similarity). DNA-DNA hybridization between strain GH1(T) and O. valericigenes DSM 18026(T) showed 24% reassociation. The major fatty acids were iso-C13:0 (13.0%), iso-C15:0 (17.6%), anteiso-C15:0 (8.4%) and C14:0 (4.1%), and the cellular fatty acid methyl esters as dimethylacetals (DMAs) were C16:0 DMA (17.8%), iso-C15:0 DMA (15.2%) and C14:0 DMA (4.52%). The cell-wall peptidoglycan of strain GH1(T) contained meso-diaminopimelic acid and the major cell-wall sugar was galactose. Based on 16S rRNA gene sequence similarity, phylogenetic analysis, DNA G+C content, DNA-DNA relatedness and distinct phenotypic characteristics, strain GH1(T) is classified in the genus Oscillibacter as a member of a novel species, for which the name Oscillibacter ruminantium sp. nov. is proposed. The type strain is GH1(T) (=KCTC 15176(T)=NBRC 108824(T)=JCM 18333(T)).

Cyclin-dependent Kinase 9 Links RNA Polymerase II Transcription to Processing of Ribosomal RNA*

PubMed Central

Burger, Kaspar; Mühl, Bastian; Rohrmoser, Michaela; Coordes, Britta; Heidemann, Martin; Kellner, Markus; Gruber-Eber, Anita; Heissmeyer, Vigo; Strässer, Katja; Eick, Dirk

2013-01-01

Ribosome biogenesis is a process required for cellular growth and proliferation. Processing of ribosomal RNA (rRNA) is highly sensitive to flavopiridol, a specific inhibitor of cyclin-dependent kinase 9 (Cdk9). Cdk9 has been characterized as the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Here we studied the connection between RNAPII transcription and rRNA processing. We show that inhibition of RNAPII activity by α-amanitin specifically blocks processing of rRNA. The block is characterized by accumulation of 3′ extended unprocessed 47 S rRNAs and the entire inhibition of other 47 S rRNA-specific processing steps. The transcription rate of rRNA is moderately reduced after inhibition of Cdk9, suggesting that defective 3′ processing of rRNA negatively feeds back on RNAPI transcription. Knockdown of Cdk9 caused a strong reduction of the levels of RNAPII-transcribed U8 small nucleolar RNA, which is essential for 3′ rRNA processing in mammalian cells. Our data demonstrate a pivotal role of Cdk9 activity for coupling of RNAPII transcription with small nucleolar RNA production and rRNA processing. PMID:23744076

Fluctuations and synchrony of RNA synthesis in nucleoli.

PubMed

Pliss, Artem; Kuzmin, Andrey N; Kachynski, Aliaksandr V; Baev, Alexander; Berezney, Ronald; Prasad, Paras N

2015-06-01

Ribosomal RNA (rRNA) sequences are synthesized at exceptionally high rates and, together with ribosomal proteins (r-proteins), are utilized as building blocks for the assembly of pre-ribosomal particles. Although it is widely acknowledged that tight regulation and coordination of rRNA and r-protein production are fundamentally important for the maintenance of cellular homeostasis, still little is known about the real-time kinetics of the ribosome component synthesis in individual cells. In this communication we introduce a label-free MicroRaman spectrometric approach for monitoring rRNA synthesis in live cultured cells. Remarkably high and rapid fluctuations of rRNA production rates were revealed by this technique. Strikingly, the changes in the rRNA output were synchronous for ribosomal genes located in separate nucleoli of the same cell. Our findings call for the development of new concepts to elucidate the coordination of ribosomal components production. In this regard, numerical modeling further demonstrated that the production of rRNA and r-proteins can be coordinated, regardless of the fluctuations in rRNA synthesis. Overall, our quantitative data reveal a spectacular interplay of inherently stochastic rates of RNA synthesis and the coordination of gene expression.

Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription.

PubMed

Xie, Qiu; Li, Caihua; Song, Xiaozhen; Wu, Lihua; Jiang, Qian; Qiu, Zhiyong; Cao, Haiyan; Yu, Kaihui; Wan, Chunlei; Li, Jianting; Yang, Feng; Huang, Zebing; Niu, Bo; Jiang, Zhengwen; Zhang, Ting

2017-03-17

The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) landscape in mouse embryonic stem cells. A significant DSB enhancement was detected in the genome of these cells and a large majority of these DSBs were found in rRNA genes. Furthermore, spontaneous DSBs in cells under folate deficiency conditions were located exclusively within the rRNA gene units, representing a H3K4me1 hallmark. Enrichment H3K4me1 at the hot spots of DSB regions enhanced the recruitment of upstream binding factor (UBF) to rRNA genes, resulting in the increment of rRNA genes transcription. Supplement of folate resulted in a restored UBF binding across DNA breakage sites of rRNA genes, and normal rRNA gene transcription. In samples from neural tube defects (NTDs) with low folate level, up-regulation of rRNA gene transcription was observed, along with aberrant UBF level. Our results present a new view by which alterations in folate levels affects DNA breakage through epigenetic control leading to the regulation of rRNA gene transcription during the early stage of development. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Methane production and methanogen levels in steers that differ in residual gain.

PubMed

Freetly, H C; Lindholm-Perry, A K; Hales, K E; Brown-Brandl, T M; Kim, M; Myer, P R; Wells, J E

2015-05-01

Methane (CH4) gas released by cattle isa product of fermentation in the digestive tract. The 2 primary sites of CH4 production in ruminants are the reticulum-rumen complex and the cecum. Methane release from cattle represents a 2% to 12% loss of the energy intake. Reducing the proportion of feed energy lost as CH4 has the potential of improving feed efficiency as well as decreasing the contribution of cattle to greenhouse gas production. Feed intake and growth were measured on 132 fall-born steers for 70 d. Seven steers with extreme positive residual gain (RG) and 7 steers with extreme negative RG whose DMI was within 0.32 SD of the mean intake were selected for subsequent measurements. Enteric CH4 production was measured via indirect calorimetry. Rumen, cecum, and rectal contents were obtained from steers at slaughter for measurement of in vitro CH4 production and methanogen 16S rRNA levels. Enteric CH4 production did not differ (P = 0.11) between the positive RG (112 ± 13 L/d)and the negative RG (74 ± 13 L/d) steers. In vitro rumen methane production did not differ between positive RG(64.26 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (61.49 × 10(-5) ± 10.85 × 10(-5) mmol∙g(-1)DM∙min(-1); P = 0.86). In vitro cecum methane production did not differ between positive RG (4.24 ×10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1)) and negative RG (4.35 × 10(-5) ± 1.90 × 10(-5) mmol∙g(-1) DM∙min(-1); P = 0.97). Methanogen 16S rRNA as a percentage of the total bacteria16S rRNA did not differ between RG groups (P = 0.18). The methanogen 16S rRNA as a percentage of rumen fluid total bacteria 16S rRNA (5.3% ±3.1%) did not differ from the methanogen 16S rRNA asa percentage of cecum content total bacteria 16S rRNA(11.8% ± 3.1%; P = 0.14). The methanogen 16S rRNA as a percentage of the rectum content total bacteria 16SrRNA (0.7% ± 3.1%) was not different from the rumen content (P = 0.29) but was less than the cecum content(P = 0.01). Methanomicrobiales 16S rRNA as a percentage of total methanogen 16S rRNA did not differ across sample sites (P = 0.81); however, steers with positive RG (10.5% ± 1.6%) were more numerous than steers with negative RG (5.1% ± 1.6%; P = 0.02). Cattle that differ in RG at the same DMI do not differ in characteristics associated with CH4 production.

Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater.

PubMed

Xing, Defeng; Ren, Nanqi; Li, Qiubo; Lin, Ming; Wang, Aijie; Zhao, Lihua

2006-04-01

Two strictly anaerobic bacterial strains (YUAN-3T and X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0.4-0.8 x 1.5-8.0 microm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3T and non-aggregative growth of strain X-29 were observed at 20-44 degrees C and pH 3.5-9.0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C(16 : 0) (44.18 %) and iso-C(12 : 0) (26.67 %). The DNA G+C contents of strains YUAN-3T and X-29 were 47.8 and 49.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within the Clostridium cellulosi rRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species, Ethanoligenens harbinense gen. nov., sp. nov. The type strain of Ethanoligenens harbinense is YUAN-3T (=JCM 12961T = CGMCC 1.5033T).

Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella.

PubMed

Noar, Jesse D; Buckley, Daniel H

2009-08-01

Strain 1a22T, a nitrogen-fixing bacterium, was isolated from soil associated with the rhizosphere of a perennial grass growing in a fallow agricultural field in Ithaca, New York, USA. Analysis of the 16S rRNA gene sequence placed the strain in the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch of the Betaproteobacteria and the closest characterized relative was the type strain of Ideonella dechloratans (97.7% 16S rRNA sequence similarity). Cells of strain 1a22T were Gram-negative, motile, straight rods, which formed polyhydroxybutyrate-like granules and were positive for oxidase and weakly positive for catalase. Cells were chemo-organotrophic, unable to grow by reduction of chlorate or nitrate and grew exclusively through aerobic respiration. Growth with mannitol on N-free solid media caused the strain to produce copious amounts of slime. The G+C content of the genomic DNA was 67.4 mol%. The major cellular fatty acids were C16:1 cis-9 and C16:0 and cells contained significant amounts of the hydroxy fatty acids C10:0 3-OH, C12:0 2-OH and C12:0 3-OH. Based on DNA-DNA hybridization studies, 16S rRNA gene sequence analysis, fatty acid analysis, and morphological and physiological characteristics, strain 1a22T represents a novel species in the genus Ideonella, for which the name Ideonella azotifigens sp. nov. is proposed. The type strain of Ideonella azotifigens is 1a22T (=JCM 15503T=DSM 21438T).

Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.

PubMed

Balkwill, D L; Drake, G R; Reeves, R H; Fredrickson, J K; White, D C; Ringelberg, D B; Chandler, D P; Romine, M F; Kennedy, D W; Spadoni, C M

1997-01-01

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G + C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently defined. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).

Characterization of a Novel Association between Two Trypanosome-Specific Proteins and 5S rRNA

PubMed Central

Ciganda, Martin; Williams, Noreen

2012-01-01

P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC. PMID:22253864

RNA content in the nucleolus alters p53 acetylation via MYBBP1A

PubMed Central

Kuroda, Takao; Murayama, Akiko; Katagiri, Naohiro; Ohta, Yu-mi; Fujita, Etsuko; Masumoto, Hiroshi; Ema, Masatsugu; Takahashi, Satoru; Kimura, Keiji; Yanagisawa, Junn

2011-01-01

A number of external and internal insults disrupt nucleolar structure, and the resulting nucleolar stress stabilizes and activates p53. We show here that nucleolar disruption induces acetylation and accumulation of p53 without phosphorylation. We identified three nucleolar proteins, MYBBP1A, RPL5, and RPL11, involved in p53 acetylation and accumulation. MYBBP1A was tethered to the nucleolus through nucleolar RNA. When rRNA transcription was suppressed by nucleolar stress, MYBBP1A translocated to the nucleoplasm and facilitated p53–p300 interaction to enhance p53 acetylation. We also found that RPL5 and RPL11 were required for rRNA export from the nucleolus. Depletion of RPL5 or RPL11 blocked rRNA export and counteracted reduction of nucleolar RNA levels caused by inhibition of rRNA transcription. As a result, RPL5 or RPL11 depletion inhibited MYBBP1A translocation and p53 activation. Our observations indicated that a dynamic equilibrium between RNA generation and export regulated nucleolar RNA content. Perturbation of this balance by nucleolar stress altered the nucleolar RNA content and modulated p53 activity. PMID:21297583

Drosophila TIF-IA is required for ribosome synthesis and cell growth and is regulated by the TOR pathway.

PubMed

Grewal, Savraj S; Evans, Justin R; Edgar, Bruce A

2007-12-17

Synthesis of ribosomal RNA (rRNA) is a key step in ribosome biogenesis and is essential for cell growth. Few studies, however, have investigated rRNA synthesis regulation in vivo in multicellular organisms. Here, we present a genetic analysis of transcription initiation factor IA (TIF-IA), a conserved RNA polymerase I transcription factor. Drosophila melanogaster Tif-IA(-/-) mutants have reduced levels of rRNA synthesis and sustain a developmental arrest caused by a block in cellular growth. We find that the target of rapamycin (TOR) pathway regulates TIF-IA recruitment to rDNA. Furthermore, we show that the TOR pathway regulates rRNA synthesis in vivo and that TIF-IA overexpression can maintain rRNA transcription when TOR activity is reduced in developing larvae. We propose that TIF-IA acts in vivo as a downstream growth-regulatory target of the TOR pathway. Overexpression of TIF-IA also elevates levels of both 5S RNA and messenger RNAs encoding ribosomal proteins. Stimulation of rRNA synthesis by TIF-IA may therefore provide a feed-forward mechanism to coregulate the levels of other ribosome components.

Drosophila TIF-IA is required for ribosome synthesis and cell growth and is regulated by the TOR pathway

PubMed Central

Grewal, Savraj S.; Evans, Justin R.; Edgar, Bruce A.

2007-01-01

Synthesis of ribosomal RNA (rRNA) is a key step in ribosome biogenesis and is essential for cell growth. Few studies, however, have investigated rRNA synthesis regulation in vivo in multicellular organisms. Here, we present a genetic analysis of transcription initiation factor IA (TIF-IA), a conserved RNA polymerase I transcription factor. Drosophila melanogaster Tif-IA −/− mutants have reduced levels of rRNA synthesis and sustain a developmental arrest caused by a block in cellular growth. We find that the target of rapamycin (TOR) pathway regulates TIF-IA recruitment to rDNA. Furthermore, we show that the TOR pathway regulates rRNA synthesis in vivo and that TIF-IA overexpression can maintain rRNA transcription when TOR activity is reduced in developing larvae. We propose that TIF-IA acts in vivo as a downstream growth–regulatory target of the TOR pathway. Overexpression of TIF-IA also elevates levels of both 5S RNA and messenger RNAs encoding ribosomal proteins. Stimulation of rRNA synthesis by TIF-IA may therefore provide a feed-forward mechanism to coregulate the levels of other ribosome components. PMID:18086911

Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center

PubMed Central

Willi, Jessica; Küpfer, Pascal; Evéquoz, Damien; Fernandez, Guillermo; Polacek, Norbert

2018-01-01

Abstract Intracellular levels of reactive oxygen species (ROS) increase as a consequence of oxidative stress and represent a major source of damage to biomolecules. Due to its high cellular abundance RNA is more frequently the target for oxidative damage than DNA. Nevertheless the functional consequences of damage on stable RNA are poorly understood. Using a genome-wide approach, based on 8-oxo-guanosine immunoprecipitation, we present evidence that the most abundant non-coding RNA in a cell, the ribosomal RNA (rRNA), is target for oxidative nucleobase damage by ROS. Subjecting ribosomes to oxidative stress, we demonstrate that oxidized 23S rRNA inhibits the ribosome during protein biosynthesis. Placing single oxidized nucleobases at specific position within the ribosome's catalytic center by atomic mutagenesis resulted in markedly different functional outcomes. While some active site nucleobases tolerated oxidative damage well, oxidation at others had detrimental effects on protein synthesis by inhibiting different sub-steps of the ribosomal elongation cycle. Our data provide molecular insight into the biological consequences of RNA oxidation in one of the most central cellular enzymes and reveal mechanistic insight on the role of individual active site nucleobases during translation. PMID:29309687

Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean.

PubMed

Yu, Yong; Li, Hui-Rong; Zeng, Yin-Xin

2011-04-01

A novel psychrotolerant bacterial strain, BCw111(T), was isolated from seawater samples from the Chukchi Sea in the Arctic Ocean. Cells of strain BCw111(T) were Gram-negative, motile, facultatively anaerobic, curved rods and were able to grow at 0-30 °C (optimum 23-25 °C). Strain BCw111(T) had Q-8 as the major respiratory quinone and contained iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c (28.13 %), C(16 : 0) (13.28 %) and C(17 : 1) (12.90 %) as the major cellular fatty acids. The genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BCw11(T) formed a distinct lineage within the genus Colwellia and exhibited the highest 16S rRNA gene sequence similarity with Colwellia polaris 537(T) (97.8 %) and Colwellia aestuarii SMK-10(T) (97.1 %). Based on phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Colwellia chukchiensis sp. nov., is proposed. The type strain is BCw111(T) ( = CGMCC 1.9127(T)  = LMG 25329(T)  = DSM 22576(T)).

Geodermatophilus sabuli sp. nov., a γ-radiation-resistant actinobacterium isolated from desert limestone.

PubMed

Hezbri, Karima; Ghodhbane-Gtari, Faten; Montero-Calasanz, Maria del Carmen; Sghaier, Haïtham; Rohde, Manfred; Schumann, Peter; Klenk, Hans-Peter; Gtari, Maher

2015-10-01

A novel γ-radiation-resistant and Gram-staining-positive actinobacterium designated BMG 8133T was isolated from a limestone collected in the Sahara desert of Tunisia. The strain produced dry, pale-pink colonies with an optimum growth at 35–40 °C and pH 6.5–8.0. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The main polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and one unspecified glycolipid. MK-9(H4) was the dominant menaquinone. Galactose and glucose were detected as diagnostic sugars. The major cellular fatty acids were branched-chain saturated acids iso-C16 : 0 and iso-C15 : 0. The DNA G+C content of the novel strain was 74.5 %. The 16S rRNA gene sequence showed highest sequence identity with Geodermatophilus ruber (98.3 %). Based on phenotypic results and 16S rRNA gene sequence analysis, strain BMG 8133T is proposed to represent a novel species, Geodermatophilus sabuli sp. nov. The type strain is BMG 8133T ( = DSM 46844T = CECT 8820T).

Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community

PubMed Central

Patel, Nisha B.; Tito, Raul Y.; Obregón-Tito, Alexandra J.; O'Neal, Lindsey; Trujillo-Villaroel, Omar; Marin-Reyes, Luis; Troncoso-Corzo, Luzmila; Guija-Poma, Emilio; Lewis, Cecil M.

2016-01-01

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T). PMID:26907921

Paenibacillus beijingensis sp. nov., a novel nitrogen-fixing species isolated from jujube garden soil.

PubMed

Gao, Miao; Xie, Lin-qi; Wang, Ya-xiong; Chen, Jian; Xu, Jing; Zhang, Xiao-xia; Sui, Xin-hua; Gao, Jun-lian; Sun, Jian-guang

2012-11-01

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 7188(T), was isolated from jujube rhizosphere soil in Beijing, China. The strain grew at 4-40 °C and pH 6-12, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 7188(T) is a member of the genus Paenibacillus. Levels of 16S rRNA gene sequence similarities between strain 7188(T) and the type strains of all recognized members of the genus Paenibacillus were below 96 %. The major cellular fatty acids were anteiso-C(15:0), anteiso-C(17:0) and C(16:0). The predominant menaquinone was MK-7. The DNA G+C content of strain 7188(T) was 60.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The diamino acid in the cell wall peptidoglycan is meso-diaminopimelic acid. On the basis of these results, strain 7188(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. is proposed. The type strain is 7188(T) (=ACCC 03082(T) = DSM 24997(T)).

Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1.

PubMed

Ishikawa, Morio; Nakajima, Kazuyuki; Itamiya, Yuko; Furukawa, Sayumi; Yamamoto, Yasushi; Yamasato, Kazuhide

2005-11-01

Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: approximately 55 % at the optimal growth pH of 8.0, greater than approximately 70 % at pH 7.0 and less than approximately 30 % at pH 9.0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2.0-3.0 % (w/v), with a range of 0-25.5 %. The optimum pH for growth was 8.0-9.5, with a range of 6.0-10.0. The G+C content of the DNA was 38.5-40.7 mol%. The isolates constituted two genomic species (DNA-DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes contained meso-diaminopimelic acid. The major cellular fatty acids were C(16 : 0) and a-C(13 : 0). Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1, with 94.8-95.1 % similarity to the genus Paraliobacillus, 93.7-94.1 % to the genus Gracilibacillus and 93.8-94.2 % to Virgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid bacteria within Bacillus rRNA group 1, chemotaxonomic characteristics and phylogenetic independence, a new genus and two species, Halolactibacillus halophilus gen. nov., sp. nov. and Halolatibacillus miurensis sp. nov., are proposed. The type strains are Halolactibacillus halophilus M2-2T (=DSM 17073T=IAM 15242T=NBRC 100868T=NRIC 0628T) (G+C content 40.2 mol%) and Halolactibacillus miurensis M23-1T (=DSM 17074T=IAM 15247T=NBRC 100873T=NRIC 0633T) (G+C content 38.5 mol%).

5S rRNA-derived and tRNA-derived SINEs in fruit bats.

PubMed

Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

2009-05-01

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.

Psychromicrobium silvestre gen. nov., sp. nov., an actinobacterium isolated from alpine forest soils.

PubMed

Schumann, Peter; Zhang, De-Chao; França, Luís; Albuquerque, Luciana; da Costa, Milton S; Margesin, Rosa

2017-03-01

Two Gram-stain-variable, non-motile, catalase-positive and cytochrome c oxidase-negative bacteria, designated AK20-18 T and AM20-54, were isolated from forest soil samples collected in the Italian Alps. Growth occurred at a temperature range of 5-30 °C, at pH 6-9 and in the presence of 0-5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strains AK20-18 T and AM20-54 was 100 %. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain AK20-18 T had highest 16S rRNA gene sequence similarity with the type strain of Arthrobacter psychrochitiniphilus (96.9 %). The cell-wall peptidoglycan structure of strain AK20-18 T was of the type A3alpha l-Lys-l-Thr-l-Ala2 (A11.27). The whole-cell sugars were galactose, ribose and lesser amounts of mannose. The major respiratory quinone of the two strains was menaquinone 9(H2) [MK-9(H2)], whereas MK-10(H2) was a minor component. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown glycolipids. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 59.9 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strains AK20-18 T and AM20-54 represent a novel genus and species, for which the name Psychromicrobium silvestre gen. nov., sp. nov. is proposed. The type strain of Psychromicrobium silvestregen. nov., sp. nov. is AK20-18 T (=DSM 102047 T =LMG 29369 T ).

Mucilaginibacter antarcticus sp. nov., isolated from tundra soil.

PubMed

Zheng, Ruichen; Zhao, Yiming; Wang, Liqiu; Chang, Xulu; Zhang, Yumin; Da, Xuyang; Peng, Fang

2016-12-01

The novel, pale yellow bacterial strain, designated S14-88T, was isolated from a tundra soil near Antarctic Peninsula, South Shetland Islands, and its taxonomic position was investigated by a genotypic and phenotypic analysis. Cells were facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped. Growth occurred at 4-28 °C (optimum at 15 °C), at pH 7.0-8.0 (optimum at 7.0) and with 0-0.6 % (w/v) NaCl (optimum, no NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S14-88T formed a lineage within the genus Mucilaginibacter. The 16S rRNA gene sequence similarity between strain S14-88T and the type strains of related species ranged from 92.2 to 96.5 %, and the 16S rRNA gene sequence of S14-88T showed highest similarity of 96.5 % to Mucilaginibacter soyangensis HME6664T. The major cellular fatty acids of strain S14-88T were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone was menaquinone MK-7, and the main polar lipid was phosphatidylethanolamine. The DNA G+C content of strain S14-88T was 42.3 mol%. On the basis of the evidence presented in this study, strain S14-88T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter antarcticus sp. nov. is proposed. The type strain is S14-88T (=CCTCC AB 2015321T=KCTC 52232T).

A korarchaeal genome reveals insights into the evolution of the Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Iain J; Elkins, James G.; Podar, Mircea

2008-06-05

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name,"Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent. Ofmore » the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.« less

A Korarchael Genome Reveals Insights into the Evolution of the Archaea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapidus, Alla; Elkins, James G.; Podar, Mircea

2008-01-07

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, ?Candidatus Korarchaeum cryptofilum,? which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent.more » Of the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.« less

Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

PubMed

Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

2010-11-01

MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

PubMed Central

Whiteley, Andrew S.; Bailey, Mark J.

2000-01-01

The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCR-based denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the α, β and γ subclasses of the class Proteobacteria [α-, β-, and γ-Proteobacteria, respectively], the Cytophaga-Flavobacterium group, and the Pseudomonas group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the Cytophaga-Flavobacterium group and to the γ-Proteobacteria. The α subclass Proteobacteria were of low relative abundance throughout the treatment system whilst the β subclass of the Proteobacteria exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The γ subclass of the Proteobacteria had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the Cytophaga-Flavobacterium group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical parameters. The potential importance of the γ-Proteobacteria and the Cytophaga-Flavobacteria during this bioremediation process was highlighted. PMID:10831417

Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium.

PubMed

Doronina, N V; Trotsenko, Y A; Krausova, V I; Boulygina, E S; Tourova, T P

1998-10-01

A new genus, Methylopila, and one new species are described for a group of seven strains of facultatively methylotrophic bacteria with the serine pathway of C1 assimilation. These bacteria are aerobic, Gram-negative, non-spore--forming, motile, colourless rods that multiply by binary fission. Their DNA base content ranges from 66 to 70 mol % G + C. Their cellular fatty acid profile consists primarily of C18:1 omega 7 cis-vaccenic and C19:0 cyclopropane acids. The major hydroxy acid is 3-OH C14:0. The main ubiquinone is Q-10. The dominant cellular phospholipids are phosphatidylethanolamine and phosphatidylcholine. The new isolates have a low level of DNA-DNA homology (5-10%) with the type strains of the serine pathway methylobacteria belonging to the genera Methylobacterium, Aminobacter, Hyphomicrobium and Methylorhabdus. Another approach, involving 16S rRNA gene sequence analysis of strain IM1T, has shown that the new isolates represent a separate branch within the alpha-2 subclass of the Proteobacteria. The type species of the new genus is Methylopila capsulata sp. nov., with the type strain IM1T (= VKM B-1606T).

Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei.

PubMed

Sharma, Subed Chandra Dev; Feng, Cuijie; Li, Jiangwei; Hu, Anyi; Wang, Han; Qin, Dan; Yu, Chang-Ping

2016-09-29

A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9-1.3 μm in length and 0.4-0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568.

FunGene: the functional gene pipeline and repository.

PubMed

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

rRNA and Poly-β-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles

PubMed Central

Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

2006-01-01

Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-β-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological advantage. PMID:16597926

rRNA and poly-beta-hydroxybutyrate dynamics in bioreactors subjected to feast and famine cycles.

PubMed

Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

2006-04-01

Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-beta-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological advantage.

Differential enrichment of TTF-I and Tip5 in the T-like promoter structures of the rDNA contribute to the epigenetic response of Cyprinus carpio during environmental adaptation.

PubMed

Nardocci, Gino; Simonet, Nicolas G; Navarro, Cristina; Längst, Gernot; Alvarez, Marco

2016-08-01

To ensure homeostasis, ectothermic organisms adapt to environmental variations through molecular mechanisms. We previously reported that during the seasonal acclimatization of the common carp Cyprinus carpio, molecular and cellular functions are reprogrammed, resulting in distinctive traits. Importantly, the carp undergoes a drastic rearrangement of nucleolar components during adaptation. This ultrastructural feature reflects a fine modulation of rRNA gene transcription. Specifically, we identified the involvement of the transcription termination factor I (TTF-I) and Tip-5 (member of nucleolar remodeling complex, NoRC) in the control of rRNA transcription. Our results suggest that differential Tip5 enrichment is essential for silencing carp ribosomal genes and that the T0 element is key for regulating the ribosomal gene during the acclimatization process. Interestingly, the expression and content of Tip5 were significantly higher in winter than in summer. Since carp ribosomal gene expression is lower in the winter than in summer, and considering that expression concomitantly occurs with nucleolar ultrastructural changes of the acclimatization process, these results indicate that Tip5 importantly contributes to silencing the ribosomal genes. In conclusion, the current study provides novel evidence on the contributions of TTF-I and NoRC in the environmental reprogramming of ribosomal genes during the seasonal adaptation process in carp.

Actinomyces vulturis sp. nov., isolated from Gyps himalayensis.

PubMed

Meng, Xiangli; Lu, Shan; Wang, Yiting; Lai, Xin-He; Wen, Yumeng; Jin, Dong; Yang, Jing; Bai, Xiangning; Zhang, Gui; Pu, Ji; Lan, Ruiting; Xu, Jianguo

2017-06-01

Two strains of Gram-stain-positive, facultatively anaerobic, non-spore-forming short rods (VUL7T and VUL8) were isolated from rectal swabs of Old World vultures, namely Gyps himalayensis, in Tibet-Qinghai Plateau, China. Optimal growth occurred at 37 °C, pH 6-7, with 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences classified the two strains to the genus Actinomyces, with highest 16S rRNA gene sequence similarity (95 %) to type strains of Actinomyces haliotis, Actinomyces radicidentis and Actinomyces urogenitalis. The major cellular fatty acids were C18 : 1ω9c and C16 : 0. MK-10(H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 54.4 mol%. DNA-DNA hybridization values with the most closely related species ofthe genusActinomyces was 24.6 %. The two strains can be differentiated from the most closely related species such as A. haliotis, A. radicidentis, A. graevenitzii and A. urogenitalis by a list of carbohydrate fermentations and enzyme activities. On the basis of physiological, biochemical and phylogenetic analysis, strains VUL7T and VUL8 represent novel species of the genus Actinomyces, for which the name Actinomyces vulturis sp. nov. is proposed. The type strain is VUL7T (=CGMCC 4.7366T=DSM 103437T).

Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite.

PubMed

Choi, Jessica K; Shah, Madhavi; Yee, Nathan

2016-10-01

A Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae. Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).

Arthrobacter ruber sp. nov., isolated from glacier ice.

PubMed

Liu, Qing; Xin, Yu-Hua; Chen, Xiu-Ling; Liu, Hong-Can; Zhou, Yu-Guang; Chen, Wen-Xin

2018-05-01

A Gram-stain-positive strain designated MDB1-42 T was isolated from ice collected from Midui glacier in Tibet, PR China. Strain MDB1-42 T was catalase-positive, oxidase-negative and grew optimally at 25-28 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that MDB1-42 T represented a member of the genus Arthrobacter. The highest level of 16S rRNA gene sequence similarity (99.86 %) was found with Arthrobacter agilis NBRC 15319 T . Multilocus sequence analysis revealed low similarity of 91.93 % between MDB1-42 T and Arthrobacter agilis NBRC 15319 T . Average nucleotide identity and digital DNA-DNA hybridization values between MDB1-42 T and the most closely related strain, Arthrobacter agilis DSM 20550 T , were 81.36 and 24.5 %, respectively. The genomic DNA G+C content was 69.0 mol%. The major cellular fatty acids of MDB1-42 T were anteiso-C15 : 0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid and one unidentified lipid. The predominant menaquinone was MK-9(H2). On the basis of results obtained using a polyphasic approach, a novel species Arthrobacter ruber sp. nov. is proposed, with MDB1-42 T (=CGMCC 1.9772 T =NBRC 113088 T ) as the type strain.

Micrococcus lactis sp. nov., isolated from dairy industry waste.

PubMed

Chittpurna; Singh, Pradip K; Verma, Dipti; Pinnaka, Anil Kumar; Mayilraj, Shanmugam; Korpole, Suresh

2011-12-01

A Gram-positive, yellow-pigmented, actinobacterial strain, DW152(T), was isolated from a dairy industry effluent treatment plant. 16S rRNA gene sequence analysis indicated that strain DW152(T) exhibited low similarity with many species with validly published names belonging to the genera Micrococcus and Arthrobacter. However, phenotypic properties including chemotaxonomic markers affiliated strain DW152(T) to the genus Micrococcus. Strain DW152(T) had ai-C(15:0) and i-C(15:0) as major cellular fatty acids, and MK-8(H(2)) as the major menaquinone. The cell-wall peptidoglycan of strain DW152(T) had l-lysine as the diagnostic amino acid and the type was A4α. The DNA G+C content of strain DW152(T) was 68.0 mol%. In 16S rRNA gene sequence analysis, strain DW152(T) exhibited significant similarity with Micrococcus terreus NBRC 104258(T), but the mean value of DNA-DNA relatedness between these strains was only 42.3%. Moreover, strain DW152(T) differed in biochemical and chemotaxonomic characteristics from M. terreus and other species of the genus Micrococcus. Based on the above differences, we conclude that strain DW152(T) should be treated as a novel species of the genus Micrococcus, for which the name Micrococcus lactis sp. nov. is proposed. The type strain of Micrococcus lactis sp. nov. is DW152(T) (=MTCC10523(T) =DSM 23694(T)).

[Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing].

PubMed

Karaevskaia, E S; Demchenko, L S; Demidov, N É; Rivkina, E M; Bulat, S A; Gilichinskiĭ, D A

2014-01-01

Archaeal communities of permafrost deposits of King George Island and Bunger Hills Oasis (Antarctica) differing in the content of biogenic methane were analyzed using clone libraries of two 16S rRNA gene regions. Phylotypes belonging to methanogenic archaea were identified in all horizons.

The complete mitochondrial genome of Chrysopa pallens (Insecta, Neuroptera, Chrysopidae).

PubMed

He, Kun; Chen, Zhe; Yu, Dan-Na; Zhang, Jia-Yong

2012-10-01

The complete mitochondrial genome of Chrysopa pallens (Neuroptera, Chrysopidae) was sequenced. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA (rRNA) genes, and a control region (AT-rich region). The total length of C. pallens mitogenome is 16,723 bp with 79.5% AT content, and the length of control region is 1905 bp with 89.1% AT content. The non-coding regions of C. pallens include control region between 12S rRNA and trnI genes, and a 75-bp space region between trnI and trnQ genes.

Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis

PubMed Central

Liiv, Aivar; Karitkina, Diana; Maiväli, Ülo; Remme, Jaanus

2005-01-01

Background The ribosome is a two-subunit enzyme known to exhibit structural dynamism during protein synthesis. The intersubunit bridges have been proposed to play important roles in decoding, translocation, and the peptidyl transferase reaction; yet the physical nature of their contributions is ill understood. An intriguing intersubunit bridge, B2a, which contains 23S rRNA helix 69 as a major component, has been implicated by proximity in a number of catalytically important regions. In addition to contacting the small ribosomal subunit, helix 69 contacts both the A and P site tRNAs and several translation factors. Results We scanned the loop of helix 69 by mutagenesis and analyzed the mutant ribosomes using a plasmid-borne IPTG-inducible expression system. We assayed the effects of 23S rRNA mutations on cell growth, contribution of mutant ribosomes to cellular polysome pools and the ability of mutant ribosomes to function in cell-free translation. Mutations A1912G, and A1919G have very strong growth phenotypes, are inactive during in vitro protein synthesis, and under-represented in the polysomes. Mutation Ψ1917C has a very strong growth phenotype and leads to a general depletion of the cellular polysome pool. Mutation A1916G, having a modest growth phenotype, is apparently defective in the assembly of the 70S ribosome. Conclusion Mutations A1912G, A1919G, and Ψ1917C of 23S rRNA strongly inhibit translation. Mutation A1916G causes a defect in the 50S subunit or 70S formation. Mutations Ψ1911C, A1913G, C1914A, Ψ1915C, and A1918G lack clear phenotypes. PMID:16053518

Uncultivated Microbial Eukaryotic Diversity: A Method to Link ssu rRNA Gene Sequences with Morphology

PubMed Central

Hirst, Marissa B.; Kita, Kelley N.; Dawson, Scott C.

2011-01-01

Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA “phylotypes” from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH) with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of novel lineages, identified in diverse environments. PMID:22174774

Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents.

PubMed

Killer, J; Havlík, J; Vlková, E; Rada, V; Pechar, R; Benada, O; Kopečný, J; Kofroňová, O; Sechovcová, H

2014-05-01

Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of Lactobacillus gasseri ATCC 33323T and Lactobacillus johnsonii ATCC 33200T (97.3% and 97.2% sequence similarities, respectively). The novel strains shared 99.2-99.6% 16S rRNA gene sequence similarities. Type strains of L. gasseri and L. johnsonii were also most related to the newly isolated strains according to rpoA (83.9-84.0% similarities), pheS (84.6-87.8%), atpA (86.2-87.7%), hsp60 (89.4-90.4%) and tuf (92.7-93.6%) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus Lactobacillus. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1T (=DSM 24759T=CCM 7945T).

Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome

PubMed Central

Polikanov, Yury S.; Osterman, Ilya A.; Szal, Teresa; Tashlitsky, Vadim N.; Serebryakova, Marina V.; Kusochek, Pavel; Bulkley, David; Malanicheva, Irina A.; Efimenko, Tatyana A.; Efremenkova, Olga V.; Konevega, Andrey L.; Shaw, Karen J.; Bogdanov, Alexey A.; Rodnina, Marina V.; Dontsova, Olga A.; Mankin, Alexander S.; Steitz, Thomas A.; Sergiev, Petr V.

2014-01-01

SUMMARY We demonstrate that the antibiotic amicoumacin A (AMI) whose cellular target was unknown, is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 Å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G. PMID:25306919

Prevotella timonensis sp. nov., isolated from a human breast abscess.

PubMed

Glazunova, Olga O; Launay, Thierry; Raoult, Didier; Roux, Véronique

2007-04-01

Gram-negative anaerobic rods were isolated from a human breast abscess. Based on genotypic and phenotypic characteristics, the novel strain belonged to the genus Prevotella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that it was closely related to Prevotella buccalis (94 % 16S rRNA gene sequence similarity), Prevotella salivae (90 %) and Prevotella oris (89.1 %). The major cellular fatty acid was C(14 : 0) (19.5 %). The new isolate represents a novel species in the genus Prevotella, for which the name Prevotella timonensis sp. nov. is proposed. The type strain is strain 4401737(T) (=CIP 108522(T)=CCUG 50105(T)).

Detection and Identification of Gastrointestinal Lactobacillus Species by Using Denaturing Gradient Gel Electrophoresis and Species-Specific PCR Primers

PubMed Central

Walter, J.; Tannock, G. W.; Tilsala-Timisjarvi, A.; Rodtong, S.; Loach, D. M.; Munro, K.; Alatossava, T.

2000-01-01

Denaturing gradient gel electrophoresis (DGGE) of DNA fragments obtained by PCR amplification of the V2-V3 region of the 16S rRNA gene was used to detect the presence of Lactobacillus species in the stomach contents of mice. Lactobacillus isolates cultured from human and porcine gastrointestinal samples were identified to the species level by using a combination of DGGE and species-specific PCR primers that targeted 16S-23S rRNA intergenic spacer region or 16S rRNA gene sequences. The identifications obtained by this approach were confirmed by sequencing the V2-V3 region of the 16S rRNA gene and by a BLAST search of the GenBank database. PMID:10618239

Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere.

PubMed

Kimura, Hiroyuki; Ishibashi, Jun-Ichiro; Masuda, Harue; Kato, Kenji; Hanada, Satoshi

2007-04-01

International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.

Sulfuricaulis limicola gen. nov., sp. nov., a sulfur oxidizer isolated from a lake.

PubMed

Kojima, Hisaya; Watanabe, Tomohiro; Fukui, Manabu

2016-01-01

A novel sulfur-oxidizing bacterium, strain HA5T, was isolated from sediment of a lake in Japan. The cells were rod-shaped (0.3-0.5 × 1.2-6.0 μm) and Gram-stain-negative. The G+C content of the genomic DNA was 63 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain oxidized thiosulfate, tetrathionate and elemental sulfur as electron donors to support autotrophic growth. Growth was observed at a temperature range of 8-37 °C, with optimum growth at 28-32 °C. The pH range for growth was pH 6.1-9.2. Optimum growth of the isolate was observed in medium without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Acidiferrobacteraceae in the class Gammaproteobacteria. The closest relative was Sulfurifustis variabilis skN76T with the highest 16S rRNA gene sequence similarity of 93 %. On the basis of phylogenetic and phenotypic properties, strain HA5T is proposed to represent a novel species of a new genus, Sulfuricaulis limicola gen. nov., sp. nov. The type strain of the type species is HA5T ( = DSM 100373T = NBRC 110752T).

Brevibacillus sediminis sp. nov., isolated from a hot spring.

PubMed

Xian, Wen-Dong; Yin, Yi-Rui; Liu, Lan; Yuan, Chang-Guo; Hussain, Firasat; Khan, Inamullah; Habib, Neeli; Zhou, En-Min; Li, Wen-Jun

2016-02-01

Strain YIM 78300 T , a novel Gram-stain-positive, moderately thermophilic, endospore-forming, rod-shaped, motile bacterium, was recovered from the sediment of a hot spring in the Tagejia Geothermal Field, Angren, Tibet province, western China. Optimum growth was observed at 50-55 °C, at pH 7.0 and with 0-1.5 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence of strain YIM 78300 T indicated that it belongs to the genus Brevibacillus . Similarity levels between the 16S rRNA gene sequences of the new isolate and those of the type strains of Brevibacillus members were 96.9-96.3 %; highest sequence similarity was with Brevibacillus thermoruber DSM 7064 T . The predominant menaquinone was MK-7 and the major cellular fatty acids were iso-C 15 : 0 and iso-C 17 : 0 . The major polar lipids were phosphatidyl- N -methylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified phospholipids, an unidentified aminophospholipid and two unidentified polar lipids. The G+C content of the genomic DNA of strain YIM 78300 T was 57.9 mol%. Based on phylogenetic analyses, and physiological and biochemical characteristics, strain YIM 78300 T is considered to represent a novel species of the genus Brevibacillus , for which the name Brevibacillus sediminis sp. nov. is proposed. The type strain is YIM 78300 T ( = DSM 29928 T  = CPCC 100738 T ).

Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill.

PubMed

Mulet, Magdalena; Sánchez, David; Rodríguez, Ana C; Nogales, Balbina; Bosch, Rafael; Busquets, Antonio; Gomila, Margarita; Lalucat, Jorge; García-Valdés, Elena

2018-04-11

Strains V113 T , V92 and V120 have been isolated from sand samples taken at the Atlantic intertidal shore in Galicia, Spain, after the Prestige oil spill. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus, but they were distinct from any known Pseudomonas species. They were extensively characterized by a polyphasic taxonomic approach and phylogenetic data that confirmed that these strains belonged to the Pseudomonas pertucinogena group. Phylogenetic analysis of 16S rRNA, gyrB and rpoD gene sequences showed that the three strains were 99% similar and were closely related to members of the P. pertucinogena group, with less than 94% similarity to strains of established species; Pseudomonas pachastrellae was the closest relative. The Average Nucleotide Index based on blast values was 89.0% between V113 T and the P. pachastrellae type strain, below the accepted species level (95%). The predominant cellular fatty acid contents and whole cell protein profiles determined by MALDI-TOF mass spectrometry also differentiated the studied strains from known Pseudomonas species. We therefore conclude that strains V113 T , V92 and V120 represent a novel species of Pseudomonas, for which the name Pseudomonas gallaeciensis is proposed; the type strain is V113 T (=CCUG 67583 T =LMG 29038 T ). Copyright © 2018 Elsevier GmbH. All rights reserved.

Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus.

PubMed

Yang, Guiqin; Zhou, Xuemei; Zhou, Shungui; Yang, Dehui; Wang, Yueqiang; Wang, Dingmei

2013-10-01

A novel thermotolerant bacterium, designated SgZ-8(T), was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20-65 °C (optimum 50 °C) and pH 6.0-9.0 (optimum 6.5-7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6-disulphonate (AQDS), fumarate and NO3(-) as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8(T) into the genus Bacillus, with the highest similarity to Bacillus badius JCM 12228(T) (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus Bacillus. The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8(T) ( = CCTCC AB 2012108(T) = KACC 16706(T)) was designated the type strain of a novel species of the genus Bacillus, for which the name Bacillus thermotolerans sp. nov. is proposed.

Saccharibacillus deserti sp. nov., isolated from desert soil.

PubMed

Sun, Ji-Quan; Wang, Xin-Ying; Wang, Li-Juan; Xu, Lian; Liu, Min; Wu, Xiao-Lei

2016-02-01

A Gram-stain-positive, facultatively anaerobic bacterial strain, designated WLJ055T, with polar and subpolar flagella was isolated from the top layer of desert soil from Erdos, Inner Mongolia, northern China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain WLJ055T was a member of the genus Saccharibacillus, and shared 97.17-97.24 % 16S rRNA gene sequence similarities with Saccharibacillus sacchari GR21T and Saccharibacillus kuerlensis HR1T. The major polar lipids of strain WLJ055T were diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone, while anteiso-C15 : 0, C16 : 0, iso-C16 : 0, and anteiso-C17 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 55.5 mol%. DNA-DNA hybridization revealed that strain WLJ055T showed 45 ± 5 % and 40 ± 5 % genomic DNA relatedness with its two closest relatives, S. sacchari GR21T and S. kuerlensis HR1T, respectively. The results of physiological and biochemical tests allowed the discrimination of strain WLJ055T from its phylogenetic relatives. Saccharibacillus deserti sp. nov. is therefore proposed to be a novel species of the genus Saccharibacillus, with strain WLJ055T ( = CGMCC 1.15276T = KCTC 33693T) as the type strain.

Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.

PubMed

Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

2013-08-01

A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Megasphaera hexanoica sp. nov., a medium-chain carboxylic acid-producing bacterium isolated from a cow rumen.

PubMed

Jeon, Byoung Seung; Kim, Seil; Sang, Byoung-In

2017-07-01

Strain MHT, a strictly anaerobic, Gram-stain-negative, non-spore-forming, spherical coccus or coccoid-shaped microorganism, was isolated from a cow rumen during a screen for hexanoic acid-producing bacteria. The microorganism grew at 30-40 °C and pH 5.5-7.5 and exhibited production of various short- and medium-chain carboxylic acids (acetic acid, butyric acid, pentanoic acid, isobutyric acid, isovaleric acid, hexanoic acid, heptanoic acid and octanoic acid), as well as H2 and CO2 as biogas. Phylogenetic analysis based on 16S rRNA gene sequencing demonstrated that MHT represents a member of the genus Megasphaera, with the closest relatives being Megapsphaera indica NMBHI-10T (94.1 % 16S rRNA sequence similarity), Megasphaera elsdenii DSM 20460T (93.8 %) and Megasphaera paucivorans DSM 16981T (93.8 %). The major cellular fatty acids produced by MHT included C12 : 0, C16 : 0, C18 : 1cis 9, and C18 : 0, and the DNA G+C content of the MHT genome is 51.8 mol%. Together, the distinctive phenotypic and phylogenetic characteristics of MHT indicate that this microorganism represents a novel species of the genus Megasphaera, for which the name Megasphaera hexanoica sp. nov. is herein proposed. The type strain of this species is MHT (=KCCM 43214T=JCM 31403T).

Lacinutrix chionocetis sp. nov., isolated from gut of a red snow crab.

PubMed

Kim, Hyangmi; Yoon, Sang-Chul; Choi, Kwang-Ho; Kim, Sung-Tae; Lee, Jae-Bong; Kim, Dong-Sun; Le Han, Ho; Bae, Kyung Sook; Park, Doo-Sang

2017-05-01

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated MAB-07 T , was isolated from the gut of a red snow crab. The novel strain grew optimally at 20 °C, pH 7.0-8.0, and in the presence of 3% (w/v) NaCl. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain MAB-07 T belongs to the type strains of species of the genus Lacinutrix. Strain MAB-07 T exhibited 16S rRNA gene sequence similarity values of 95.5-97.8% with the type strains of species of the genus Lacinutrix. The predominant cellular fatty acids of strain MAB-07 T were iso-C 15:1 G (27.5%) and iso-C 15:0 (21.7%). The major respiratory quinine was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. The genomic DNA G + C content was determined to be 33.3%, and its DNA-DNA relatedness values with the type strains of L. venerupis, L. mariniflava, L. jangbogonensis, L. algicola, and Olleya aquimaris were 28-32%. Based on the data from this polyphasic taxonomic study, strain MAB-07 T is considered to represent a novel species of the genus Lacinutrix, for which the name L. chionocetis sp. nov. is proposed. The type strain is MAB-07 T (=KCTC 42767 T  = JCM 30988 T ).

Glaciimonas frigoris sp. nov., a psychrophilic bacterium isolated from ancient Siberian permafrost sediment, and emended description of the genus Glaciimonas.

PubMed

Margesin, Rosa; Zhang, De-Chao; Frasson, David; Brouchkov, Anatoli

2016-02-01

The bacterial strain N1-38 T was isolated from ancient Siberian permafrost sediment. The strain was Gram-reaction-negative, motile by gliding, rod-shaped and psychrophilic, and showed good growth over a temperature range of - 5 to 25 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain N1-38 T was most closely related to members of the genus Glaciimonas and shared the highest 16S rRNA gene sequence similarities with the type strains of Glaciimonas alpina (99.3 %), Glaciimonas immobilis (98.9 %) and Glaciimonas singularis (96.5 %). The predominant cellular fatty acids of strain N1-38 T were summed feature 3 (C 16 : 1 ω7 c and/or iso-C 15 : 0 2-OH), C 16 : 0 and C 18 : 1 ω7 c . The major respiratory quinone was ubiquinone 8 and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genomic DNA G+C content was 53.0 mol%. Combined data of phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain N1-38 T represents a novel species of the genus Glaciimonas , for which the name Glaciimonas frigoris sp. nov. is proposed. The type strain is N1-38 T ( = LMG 28868 T  = CCOS 838 T ). An emended description of the genus Glaciimonas is also provided.

Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates.

PubMed

Jumas-Bilak, Estelle; Bouvet, Philippe; Allen-Vercoe, Emma; Aujoulat, Fabien; Lawson, Paul A; Jean-Pierre, Hélène; Marchandin, Hélène

2015-11-01

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5-91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

Micrococcus cohnii sp. nov., isolated from the air in a medical practice.

PubMed

Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

2013-01-01

Three Gram-reaction-positive bacteria, isolated from the air in a medical practice (strains WS4601(T), WS4602) or a pharmaceutical clean room (strain WS4599), were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences of the three novel strains showed that they formed a distinct lineage within the genus Micrococcus, sharing 16S rRNA gene sequence similarities of 96.1-98.0 % with other species of this genus. Chemotaxonomic features also supported the classification of the three novel strains within the genus Micrococcus. The major cellular fatty acids of strain WS4601(T) were anteiso-C(15 : 0) and iso-C(15 : 0), the cell-wall peptidoglycan was of type A3α (L-Lys-L-Ala), and the predominant respiratory quinones were MK-7(H(2)) and MK-8(H(2)). The polar lipid profile contained diphosphatidylglycerol and phosphatidylglycerol, but no phosphatidylinositol. The G+C content of the genomic DNA was 70.4 mol%. Numerous physiological properties were found that clearly distinguished strains WS4599, WS4601(T) and WS4602 from established members of the genus Micrococcus. Based on the phenotypic and phylogenetic data, strains WS4599, WS4601(T) and WS4602 are considered to represent three different strains of a novel species of the genus Micrococcus, for which the name Micrococcus cohnii sp. nov. is proposed. The type strain is WS4601(T) (=DSM 23974(T)=LMG 26183(T)).

Mucilaginibacter vulcanisilvae sp. nov., isolated from a volcanic forest.

PubMed

Baek, Kyunghwa; Ok Jeon, Che

2015-07-01

A Gram-stain-negative, strictly aerobic, pale-pink-pigmented bacterium, designated strain G27(T), was isolated from a volcanic forest of Jeju Island, South Korea. Cells were catalase- and oxidase-positive, non-motile rods producing exopolysaccharide and flexirubin-type and pale pink pigments. Growth of strain G27(T) was observed at 4-30 °C (optimum, 25 °C) and pH 5.0-8.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G27(T) formed a phyletic lineage within the genus Mucilaginibacter of the family Sphingobacteriaceae. Strain G27(T) was related most closely to Mucilaginibacter gossypii Gh-67(T) at 96.5% 16S rRNA gene sequence similarity. Strain G27(T) contained menaquinone 7 (MK-7) as the sole isoprenoid quinone and summed feature 3 (comprising C16:1ω7c/C16:1ω6c), iso-C15:0, C16:0, C16:1ω5c and C16:1ω5c as the major cellular fatty acids. Phosphatidylethanolamine was identified as the major polar lipid. The G+C content of the genomic DNA was 46.5 mol%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G27(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter vulcanisilvae sp. nov. is proposed. The type strain is G27(T) ( = KACC 18231(T) = JCM 30363(T)).

Luteibacter jiangsuensis sp. nov.: a methamidophos-degrading bacterium isolated from a methamidophos-manufacturing factory.

PubMed

Wang, Li; Wang, Guang-li; Li, Shun-peng; Jiang, Jian-dong

2011-01-01

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, JW-64-1(T), capable of degrading methamidophos was isolated from a methamidophos-manufacturing factory in China, and was subjected to a polyphasic taxonomic investigation. Strain JW-64-1(T) produced circular, smooth, transparent, yellow-colored colonies (1.0-2.0 mm) on LB agar after 2 days incubation. It grew optimally at 25-30°C and pH 7.0 without the presence of NaCl. The G+C content of the total DNA was 63.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW-64-1(T) fell within the cluster comprising Luteibacter species. The 16S rRNA gene sequence of strain JW-64-1(T) was most closely related to Luteibacter rhizovicinus DSM 16549(T) (98.6%), followed by Luteibacter yeojuensis DSM 17673(T) (98.4%) and L. anthropi CCUG 25036(T) (98.2%). The major cellular fatty acids of strain JW-64-1(T) were iso-C(15:0) (24.1%), iso-C(17:0) (20.2%) and summed feature 9 comprising iso-C(17:1) ω9c and/or C(16:0) 10-methyl (20.3%). The major isoprenoid quinine was Q-8 (98%), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipids-1, aminolipids-2, and phospholipids. The values for DNA-DNA relatedness between strain JW-64-1(T) and the closest phylogenetic relatives of L. rhizovicinus and Luteibacter yeojuensis were 34.8 ± 2.6 and 25.6 ± 3.1%, respectively. On the basis of the phenotypic, chemotaxonomic, DNA-DNA relatedness and phylogenetic analysis based on the 16S rRNA gene sequences, strain JW-64-1(T) represents a novel species of the genus Luteibacter, for which the name Luteibacter jiangsuensis sp. nov. is proposed. The type strain is JW-64-1(T) (=CGMCC 1.10133(T) = DSM 22396(T)).

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

PubMed Central

Lässer, Cecilia; Shelke, Ganesh Vilas; Yeri, Ashish; Kim, Dae-Kyum; Crescitelli, Rossella; Raimondo, Stefania; Sjöstrand, Margareta; Gho, Yong Song; Van Keuren Jensen, Kendall; Lötvall, Jan

2017-01-01

ABSTRACT Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analyzed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the 2 exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions. PMID:27791479

Salininema proteolyticum gen. nov., sp. nov., a halophilic rare actinomycete isolated from wetland soil, and emended description of the family Glycomycetaceae.

PubMed

Nikou, Mahdi Moshtaghi; Ramezani, Mohaddaseh; Amoozegar, Mohammad Ali; Rasouli, Mehrnoush; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; de la Haba, Rafael R; Ventosa, Antonio

2015-10-01

A Gram-stain-positive actinobacterial strain, Miq-4T, was isolated from soil around Meighan wetland in the centre of Iran. Strain Miq-4T was strictly aerobic, catalase- and oxidase-positive. The isolate grew in the presence of 3–15 % (w/v) NaCl, at 20–40 °C and pH 6.0–11.0. The optimum NaCl, temperature and pH for growth were 7.0 %, 30 °C and 7.0–8.5, respectively. The cell wall of strain Miq-4T contained meso-diaminopimelic acid as the diamino acid and glucose and ribose as the whole-cell sugars. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Strain Miq-4T synthesized cellular fatty acids of anteiso- and iso-branched types, including anteiso-C17 : 0, anteiso- C15 : 0 and iso-C16 : 0, and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and characteristic patterns of 16S rRNA gene signature nucleotides revealed that strain Miq-4T belongs to the family Glycomycetaceae and showed the closest phylogenetic similarity with Haloglycomyces albus YIM 92370T (94.1 % 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain Miq-4T represents a novel species of a new genus in the family Glycomycetaceae, for which the name Salininema proteoliyticum gen. nov., sp. nov. is proposed. The type strain of the type species is Miq-4T ( = IBRC-M 10908T = LMG 28391T). An emended description of the family Glycomycetaceae is also proposed in order to include features of the new genus.

Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand.

PubMed

Pakdeeto, Amnat; Tanasupawat, Somboon; Thawai, Chitti; Moonmangmee, Somporn; Kudo, Takuji; Itoh, Takashi

2007-02-01

Two strains of strictly aerobic, moderately halophilic Gram-positive rods were isolated from fermented shrimp paste ('ka-pi') produced in Thailand. They produced a red pigment and grew optimally in the presence of 5-30 % NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C(15 : 0). Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The DNA G+C content was 41.2-41.6 mol%. Comparative 16S rRNA gene sequence analyses showed that strain PN7-6T was most closely related to Lentibacillus salarius KCTC 3911T with 96.5 % sequence similarity. On the basis of phenotypic and molecular properties, the two isolates represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kapialis sp. nov. is proposed. The type strain is PN7-6T (=JCM 12580T=PCU 259T=TISTR 1551T).

Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand.

PubMed

Liu, Ming; Qi, Huan; Luo, Xuesong; Dai, Jun; Peng, Fang; Fang, Chengxiang

2012-01-01

A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311(T), was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311(T) was related closely to Cesiribacter andamanensis AMV16(T) (94.6% similarity). The DNA G+C content of strain 311(T) was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C(16:1)ω5c (29.9%), iso-C(15:0) (21.9%), iso-C(17:0) 3-OH (13.3%) and summed feature 4 (iso-C(17:1) I and/or anteiso-C(17:1) B; 13.0%). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311(T) is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter roseus sp. nov. is proposed. The type strain is 311(T) (=CCTCC AB 207142(T) =KACC 15456(T)).

Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology.

PubMed

Fu, Rao; Gong, Jun

2017-11-01

Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV 0.14 . The maximum growth rate could be well predicted by a combination of per-cell ribotype CN and temperature. Our empirical data and modeling on single-cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance-based interpretation of quantitative ribotype data in population and community ecology of protists. © 2017 The Authors. Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae.

PubMed

Mukherjee, Arpan; Wheaton, Garrett H; Counts, James A; Ijeomah, Brenda; Desai, Jigar; Kelly, Robert M

2017-07-01

When abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae, originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during 'uranium-shock' implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN-domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro. RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula, a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium-rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post-transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Origin and Metabolic Properties of the RNA Species Formed During the Replication Cycle of Virus 2C

PubMed Central

Cocito, C.

1974-01-01

When short pulses of [3H]uracil were administered to Bacillus subtilis infected with phage 2C, the main species of labeled RNA was a 10S component that hybridized chiefly, but not exclusively, with the heavy strand of 2C DNA. After long pulses, most of the radioactivity was found in the 23S, 16S, and 5S rRNA's, which are coded for by the cell genome. Formation of such RNA species was reduced but not suppressed upon infection, the extent of inhibition being proportional to the virus-to-cell ratio. When bacteria were incubated with virginiamycin, an inhibitor of protein synthesis, and then infected with phage 2C, formation of virus-specific RNA decreased. This antibiotic also reduced the preferential transcription of the heavy strand of 2C DNA. The methylation pattern of rRNA remained unchanged upon infection with phage 2C. Virginiamycin reduced both the methylation and stability of rRNA in uninfected cells; this effect, however, was clearly reduced during the viral cycle. It can be concluded that in 2C-infected B. subtilis, cellular and viral RNA species are simultaneously synthesized and a preferential transcription of viral message depends not only on the number of available copies of viral template, but also on their translation. Moreover, virus-dictated proteins are responsible for the inhibition of cellular RNA formation as well as for the asymmetrical transcription of phage genome. Finally, virginiamycin and phage 2C have antagonistic, nonoverlapping effects on the metabolism and function of the RNA of the host cell. PMID:4214950

Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea.

PubMed

Jung, Seo-Youn; Kang, So-Jung; Lee, Mi-Hwa; Lee, Soo-Young; Oh, Tae-Kwang; Yoon, Jung-Hoon

2005-09-01

Three Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12(T), SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25-30 degrees C and in the presence of 2-3% (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C(15:0), iso-C(17:0) 3-OH, iso-C(15:1), anteiso-C(15:0), iso-C(15:0) 3-OH and C(16:1)omega7c and/or iso-C(15:0) 2-OH. The DNA G+C contents of the three strains were 34.7-34.9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93.8-94.9% to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12(T), SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12(T) (=KCTC 12379(T)=DSM 17032(T)).

Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus.

PubMed

Meng, Xiangli; Lu, Shan; Lai, Xin-He; Wang, Yiting; Wen, Yumeng; Jin, Dong; Yang, Jing; Xu, Jianguo

2017-06-01

Two strains (VUL4_1T and VUL4_2) of Gram-staining-positive, catalase-negative, non-spore-forming short rods were isolated from rectal swabs of Old World vultures (Gypaetus barbatus) in the Tibet-Qinghai Plateau, China. Analysis of morphological characteristics and biochemical tests indicated that the two strains closely resembled each other but were distinct from other species of the genus Actinomyces previously described. Based on the results of 16S rRNA gene sequence comparison and genome analysis, strains were determined to be members of the genus Actinomyces, closely related to the type strains of Actinomyces marimammalium (96.4 % 16S rRNA gene sequence similarity), Actinomyceshongkongensis (92.4 %), Actinomyceshordeovulneris (92.3 %) and Actinomycesnasicola (92.2 %), respectively. Optimal growth conditions were 37 °C, pH 6-7, with 1 % (w/v) NaCl. Strain VUL4_1T contained C18 : 1ω9c and C16 : 0 as the major cellular fatty acids and diphosphatidylglycerol as the major component of the polar lipids. The genomic DNA G+C content of VUL4_1T was 54.9 mol%. Strain VUL4_1T showed less than 70 % DNA-DNA relatedness with other species of the genus Actinomyces, further supporting strain VUL4_1T as a representative of a novel species. Based on the phenotypic data and phylogenetic inference, a novel species, Actinomyces liubingyangii sp. nov., is proposed with VUL4_1T (=CGMCC 4.7370T=DSM 104050T) as the type strain.

Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi).

PubMed

Daroonpunt, Rungsima; Tanasupawat, Somboon; Kudo, Takuji; Ohkuma, Moriya; Itoh, Takashi

2016-04-01

A Gram-reaction-positive and rod-shaped bacterium, designated KN3-8-4T, was isolated from shrimp paste collected from a market in Nakhon Sri Thammarat province, Thailand. Strain KN3-8-4T was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a terminal position. The isolate grew at pH 4.5-10 (optimum pH 7.5), at 11-42 °C (optimum 37 °C) and in the presence of 0-15% (w/v) NaCl (optimum 1-5%). On the basis of 16S rRNA gene sequences, strain KN3-8-4T belonged to the genus Virgibacillus and showed highest similarity with Virgibacillus olivae JCM 30551T (97.85% 16S rRNA gene sequence similarity). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Strain KN3-8-4T contained anteiso-C15:0 and anteiso-C17:0 as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and one glycolipid as polar lipids. The DNA G+C content was 43.5 mol%. Strain KN3-8-4T showed low DNA-DNA relatedness (20.44%) with V. olivae JCM 30551T. On the basis of phenotypic and chemotaxonomic data and phylogenetic analyses, strain KN3-8-4T represents a novel species of the genus Virgibacillus for which the name Virgibacillus kapii sp. nov. is proposed. The type strain is KN3-8-4T (=JCM 30071T=LMG 28282T=TISTR 2279T=PCU 345T).

Piscibacillus salipiscarius gen. nov., sp. nov., a moderately halophilic bacterium from fermented fish (pla-ra) in Thailand.

PubMed

Tanasupawat, Somboon; Namwong, Sirilak; Kudo, Takuji; Itoh, Takashi

2007-07-01

A Gram-positive, spore-forming and moderately halophilic bacterium was isolated from fermented fish (pla-ra) in Thailand. Cells of the isolate, RBU1-1(T), were strictly aerobic, motile rods and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Menaquinone with seven isoprene units (MK-7) was the predominant quinone. This isolate grew at 15-48 degrees C, pH 5-9 and in 2-30 % NaCl (optimally 10-20 %). The major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). Polar lipid analysis revealed the presence of phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.7 mol%. 16S rRNA gene sequence analysis revealed that strain RBU1-1(T) was a member of the family Bacillaceae, and belonged to a cluster with Filobacillus and Tenuibacillus; strain RBU1-1(T) showed 16S rRNA gene sequence similarities of 96.0-96.9 % to members of these two genera. Strain RBU1-1(T) could also be differentiated from members of the genera Filobacillus and Tenuibacillus based on certain phenotypic characteristics such as cell-wall composition, mode of flagellation and growth pH range. Therefore, strain RBU1-1(T) is considered to represent a novel species in a new genus in the family Bacillaceae, for which the name Piscibacillus salipiscarius gen. nov., sp. nov. is proposed. The type strain of Piscibacillus salipiscarius is RBU1-1(T) (=JCM 13188(T)=PCU 270(T)=TISTR 1571(T)).

Terrimonas arctica sp. nov., isolated from Arctic tundra soil.

PubMed

Jiang, Fan; Qiu, Xia; Chang, Xulu; Qu, Zhihao; Ren, Lvzhi; Kan, Wenjing; Guo, Youhao; Fang, Chengxiang; Peng, Fang

2014-11-01

A novel, Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated R9-86(T), was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). Growth occurred at 4-28 °C (optimum, 22-25 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R9-86(T) belonged to the genus Terrimonas in the family Chitinophagaceae. 16S rRNA gene sequence similarities between strain R9-86(T) and the type strains of species of the genus Terrimonas with validly published names ranged from 93.7 to 95.0%. Strain R9-86(T) contained iso-C(15:1)-G (25.7%), iso-C(15:0) (24.5%), iso-C(17:0)-3OH (18.3%) and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c, 8.7%) as its major cellular fatty acids; phosphatidylethanolamine and an unknown polar lipid as its main polar lipids, and MK-7 as its predominant respiratory quinone. The DNA G+C content was 48.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-86(T) is considered to represent a novel species of the genus Terrimonas, for which the name Terrimonas arctica sp. nov. is proposed. The type strain is R9-86(T) ( =CCTCC AB 2011004(T) =NRRL B-59114(T)). © 2014 IUMS.

Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus.

PubMed

Chen, Yi-Guang; Zhang, Yu-Qin; Yi, Lang-Bo; Li, Zhao-Yang; Wang, Yong-Xiao; Xiao, Huai-Dong; Chen, Qi-Hui; Cui, Xiao-Long; Li, Wen-Jun

2010-03-01

A facultatively anaerobic, moderately halophilic, Gram-positive, endospore-forming, motile, catalase- and oxidase-positive, rod-shaped bacterium, strain JSM 072002(T), was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the South China Sea. Strain JSM 072002(T) was able to grow with 0.5-15 % (w/v) NaCl and at pH 6.0-10.0 and 15-50 degrees C; optimum growth was observed with 2-5 % (w/v) NaCl and at pH 7.5 and 35 degrees C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The predominant respiratory quinone was menaquinone 7 and the genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 072002(T) should be assigned to the genus Pontibacillus and revealed relatively low 16S rRNA gene sequence similarities (<97 %) with the type strains of the three recognized Pontibacillus species (Pontibacillus chungwhensis BH030062(T), 96.8 %; Pontibacillus marinus KCTC 3917(T), 96.7 %; Pontibacillus halophilus JSM 076056(T), 96.0 %). The combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 072002(T) represents a novel species of the genus Pontibacillus, for which the name Pontibacillus litoralis sp. nov. is proposed. The type strain is JSM 072002(T) (=DSM 21186(T)=KCTC 13237(T)). An emended description of the genus Pontibacillus is also presented.

Sellimonas intestinalis gen. nov., sp. nov., isolated from human faeces.

PubMed

Seo, Boram; Yoo, Ju Eun; Lee, Yung Mi; Ko, GwangPyo

2016-02-01

A Gram-stain-positive and obligately anaerobic bacterial strain, BR72 T , forming ivory yellow colonies was isolated from a faecal sample of a healthy Korean woman. 16S rRNA gene sequence analysis indicated that strain BR72 T belongs to Clostridium cluster XIVa and represents a distinct phyletic line within the family Lachnospiraceae . The most closely related strains were Clostridium nexile DSM 1787 T (94.1 % 16S rRNA gene sequence similarity), Coprococcus comes ATCC 27758 T (93.5 %), Ruminococcus torques ATCC 27756 T (93.5 %), Ruminococcus lactaris ATCC 29176 T (93.5 %), Clostridium aerotolerans DSM 5434 T (93.1 %) and Eubacterium fissicatena DSM 3598 T (92.9 %). The DNA G+C content of strain BR72 T based on its genome sequence was 45.3 mol%. The major cellular fatty acids were C 16 : 0 , C 14 : 0 , and iso-C 17 : 1 I and/or anteiso-C 17 : 1 B. Acetic acid was produced from glucose fermentation. Other physiological and biochemical comparisons allowed the phenotypic differentiation of strain BR72 T from the members of the family Lachnospiraceae . Based on the phylogenetic and phenotypic findings, this strain is considered to represent a novel species of a new genus belonging to the family Lachnospiraceae and the name Sellimonas intestinalis gen. nov., sp. nov. is proposed. The type strain of Sellimonas intestinalis is BR72 T ( = KCTC 15479 T  = JCM 30749 T ).

Proteiniborus ethanoligenes gen. nov., sp. nov., an anaerobic protein-utilizing bacterium.

PubMed

Niu, Lili; Song, Lei; Dong, Xiuzhu

2008-01-01

A novel anaerobic, mesophilic, protein-utilizing bacterial strain, GW(T), was isolated from the mesophilic hydrogen-producing granular sludge used to treat food industry wastewater. The strain was a Gram-positive, non-spore-forming and non-motile rod. Growth of the strain was observed at 20-48 degrees C and at pH 6.4-10.0. The strain used yeast extract and peptone as carbon and energy sources. Weak growth was also observed with tryptone and Casamino acids as carbon and energy sources. The strain used none of the tested carbohydrates, alcohols or fatty acids. The fermentation products in peptone-yeast broth included ethanol, acetic acid, hydrogen and carbon dioxide. Gelatin was not hydrolysed. Nitrate was reduced. Indole was produced. NH(3) and H(2)S were not produced. The DNA G+C content of strain GW(T) was 38.0 mol%. The predominant cellular fatty acids were the saturated fatty acids C(14:0) (15.58%), C(16:0) (25.40%) and C(18:0) (12.03%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain GW(T) represented a new branch within cluster XII of the Clostridium subphylum, with <89.6% 16S rRNA gene sequence similarities to all described species. On the basis of polyphasic evidence from this study, strain GW(T) represents a new genus and novel species, for which the name Proteiniborus ethanoligenes gen. nov., sp. nov. is proposed. The type strain is GW(T) (=CGMCC 1.5055(T)=JCM 14574(T)).

Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family Propionibacteriaceae isolated from a pharmaceutical clean room and from food.

PubMed

Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

2012-12-01

Four Gram-stain-positive, aerobic bacterial strains isolated from a pharmaceutical clean room (strain WS4616(T)), a dessert milk product (strain WS4617) and from raw milk (strains WS4623 and WS4624) were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences showed that they formed a distinct lineage within the family Propionibacteriaceae. Similarity values between 16S rRNA gene sequences of the four novel strains and the type species of all genera belonging to the family Propionibacteriaceae were 89.2-94.1%. The major cellular fatty acid was anteiso-C(15:0) and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were MK-8(H(4)) and MK-9(H(4)). The cell-wall peptidoglycan of type A3γ contained ll-diaminopimelic acid, alanine, glycine and glutamic acid. The G+C content of the genomic DNA of strain WS4616(T) was 67.7 mol%. The whole-cell sugar pattern contained ribose, mannose, arabinose, glucose and galactose. On the basis of phenotypic and genetic data, strains WS4616(T), WS4617, WS4623 and WS4624 are classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Naumannella halotolerans gen. nov., sp. nov. is proposed. The type strain is WS4616(T) ( = DSM 24323(T) = LMG 26184(T)) and three additional strains are WS4617, WS4623 and WS4624.

Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples

PubMed Central

Passaretti, Teresa V.; Jose, Reashma; Cole, Jocelyn; Coorevits, An; Carpenter, Andrea N.; Jose, Sherly; Van Landschoot, Anita; Izard, Jacques; Kohlerschmidt, Donna J.; Vandamme, Peter; Dewhirst, Floyd E.; Fisher, Mark A.; Musser, Kimberlee A.

2013-01-01

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica. Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria. The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria. The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed. PMID:22798652

Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments

PubMed Central

Kimura, Hiroyuki; Sugihara, Maki; Kato, Kenji; Hanada, Satoshi

2006-01-01

Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained. PMID:16391020

The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis.

PubMed

Mayer, Christine; Bierhoff, Holger; Grummt, Ingrid

2005-04-15

Cells respond to a variety of extracellular and intracellular forms of stress by down-regulating rRNA synthesis. We have investigated the mechanism underlying stress-dependent inhibition of RNA polymerase I (Pol I) transcription and show that the Pol I-specific transcription factor TIF-IA is inactivated upon stress. Inactivation is due to phosphorylation of TIF-IA by c-Jun N-terminal kinase (JNK) at a single threonine residue (Thr 200). Phosphorylation at Thr 200 impairs the interaction of TIF-IA with Pol I and the TBP-containing factor TIF-IB/SL1, thereby abrogating initiation complex formation. Moreover, TIF-IA is translocated from the nucleolus into the nucleoplasm. Substitution of Thr 200 by valine as well as knock-out of Jnk2 prevent inactivation and translocation of TIF-IA, leading to stress-resistance of Pol I transcription. Our data identify TIF-IA as a downstream target of the JNK pathway and suggest a critical role of JNK2 to protect rRNA synthesis against the harmful consequences of cellular stress.

Structure of the initiation-competent RNA polymerase I and its implication for transcription

NASA Astrophysics Data System (ADS)

Pilsl, Michael; Crucifix, Corinne; Papai, Gabor; Krupp, Ferdinand; Steinbauer, Robert; Griesenbeck, Joachim; Milkereit, Philipp; Tschochner, Herbert; Schultz, Patrick

2016-07-01

Eukaryotic RNA polymerase I (Pol I) is specialized in rRNA gene transcription synthesizing up to 60% of cellular RNA. High level rRNA production relies on efficient binding of initiation factors to the rRNA gene promoter and recruitment of Pol I complexes containing initiation factor Rrn3. Here, we determine the cryo-EM structure of the Pol I-Rrn3 complex at 7.5 Å resolution, and compare it with Rrn3-free monomeric and dimeric Pol I. We observe that Rrn3 contacts the Pol I A43/A14 stalk and subunits A190 and AC40, that association re-organizes the Rrn3 interaction interface, thereby preventing Pol I dimerization; and Rrn3-bound and monomeric Pol I differ from the dimeric enzyme in cleft opening, and localization of the A12.2 C-terminus in the active centre. Our findings thus support a dual role for Rrn3 in transcription initiation to stabilize a monomeric initiation competent Pol I and to drive pre-initiation complex formation.

Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

PubMed Central

Dewhirst, Floyd E.; Chien, Chih-Ching; Paster, Bruce J.; Ericson, Rebecca L.; Orcutt, Roger P.; Schauer, David B.; Fox, James G.

1999-01-01

The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified as Lactobacillus acidophilus (strain ASF 360), Lactobacillus salivarius (strain ASF 361), and Bacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus and Lactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in the Cytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipes phylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes, Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster, Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms. PMID:10427008

Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil.

PubMed

Ueki, Atsuko; Akasaka, Hiroshi; Satoh, Atsuya; Suzuki, Daisuke; Ueki, Katsuji

2007-08-01

Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).

Gaetbulibacter marinus sp. nov., isolated from coastal seawater, and emended description of the genus Gaetbulibacter.

PubMed

Yang, Seung-Jo; Cho, Jang-Cheon

2008-02-01

A Gram-negative, yellow-coloured, chemoheterotrophic, non-motile, strictly aerobic, rod-shaped bacterium, designated IMCC1914(T), was isolated from coastal surface seawater of the Yellow Sea, Korea. The temperature, pH and NaCl ranges for growth were 3-37 degrees C, pH 8.0-11.0 and 0.5-4.0 %. The DNA G+C content of the strain was 38.1 mol% and the major cellular fatty acids were iso-C(15 : 1) (32.1 %), iso-C(15 : 0) (20.6 %) and iso-C(17 : 0) 3-OH (7.8 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC1914(T) was related most closely to Gaetbulibacter saemankumensis SMK-12(T), with a sequence similarity of 96.2 %. On the basis of phylogenetic data and several distinct phenotypic characteristics, strain IMCC1914(T) (=KCCM 42380(T) =NBRC 102040(T)) could be assigned to the genus Gaetbulibacter as the type strain of a novel species, for which the name Gaetbulibacter marinus sp. nov. is proposed. In addition, an emended description of the genus Gaetbulibacter is presented.

A Novel Epiphytic Chlorophyll d-containing Cyanobacterium Isolated from a Mangrove-associated Red Alga.

PubMed

Larkum, Anthony W D; Chen, Min; Li, Yaqiong; Schliep, Martin; Trampe, Erik; West, John; Salih, Anya; Kühl, Michael

2012-12-01

A new habitat and a new chlorophyll (Chl) d-containing cyanobacterium belonging to the genus Acaryochloris are reported in this study. Hyperspectral microscopy showed the presence of Chl d-containing microorganisms in epiphytic biofilms on a red alga (Gelidium caulacantheum) colonizing the pneumato-phores of a temperate mangrove (Avicennia marina). The presence of Chl d was further proven by high performance liquid chromatography (HPLC)-based pigment analysis and by confocal imaging of cultured cells. Enrichment of mangrove biofilm samples under near-infrared radiation (NIR) yielded the new Acaryochloris sp. MPGRS1, which was closely related in terms of 16S rRNA gene sequence to an isolate from the hypertrophic Salton Sea, USA. The new isolate used Chl d as its major photopigment; Chl d and Chl a contents were ~98% and 1%-2% of total cellular chlorophyll, respectively. These findings expand the variety of ecological niches known to harbor Chl d-containing cyanobacteria and support our working hypothesis that such oxyphototrophs may be ubiquitous in habitats depleted of visible light, but with sufficient NIR exposure. © 2012 Phycological Society of America.

Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad.

PubMed

Montero-Calasanz, M C; Göker, M; Pötter, G; Rohde, M; Spröer, C; Schumann, P; Gorbushina, A A; Klenk, H-P

2013-03-01

A novel Gram-positive, aerobic, actinobacterial strain, CF5/5, was isolated from soil in the Sahara desert, Chad. It grew best at 20-35 °C and at pH 6.0-8.0 and with 0-4 % (w/v) NaCl, forming black-colored colonies. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G + C content was 75.9 mol%. The peptidoglycan contained meso-diaminopimelic acid; galactose and xylose were detected as diagnostic sugars. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol; MK-9(H(4)) was the dominant menaquinone. The major cellular fatty acids were: iso-C(16:0) and iso-C(15:0). The 16S rRNA gene showed 95.6-98.3 % sequence similarity with the other named members of the genus Geodermatophilus. Based on the polyphasic taxonomy data, the isolate is proposed to represent a novel species, Geodermatophilus saharensis with the type strain CF5/5(T) = DSM 45423 = CCUG 62813 = MTCC 11416.

Butyricicoccus porcorum sp. nov., a butyrate-producing bacterium from swine intestinal tract.

PubMed

Trachsel, Julian; Humphrey, Samuel; Allen, Heather K

2018-05-01

A Gram-stain-positive, non-motile, butyrate-producing coccus was cultured from the distal ileum of swine. This organism was isolated on rumen-fluid medium, consumes acetate, and produces butyrate as its major end product when grown on mono- and di-saccharides. A phylogenetic analysis based on near full-length 16S rRNA gene sequences as well as whole-genome phylogenies suggests that this isolate is most closely related to species in the genus Butyricicoccus, with Butyricicoccus pullicaecorum being the closest named relative (93.5 % 16S similarity). The G+C content of this isolate is 54 mol%, and the major cellular fatty acids are C18 : 0 DMA, C14 : 0, C18 : 1ω9c and C16 : 0. These data indicate that this isolate represents a novel species within the genus Butyricicoccus, for which the name Butyricicoccus porcorum sp. nov. is proposed. The type strain of Butyricicoccus porcorum is BB10 T (ATCC TSD-102 T , DSM 104997 T ).

Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome.

PubMed

Hynönen, Ulla; Rasinkangas, Pia; Satokari, Reetta; Paulin, Lars; de Vos, Willem M; Pietilä, Taija E; Kant, Ravi; Palva, Airi

2016-06-01

In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice.

PubMed

Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

2015-09-01

A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-A(T)) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16y(T) (98.9% similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6%. Based on data from this polyphasic analysis, strain MDB1-A(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-A(T) ( = CGMCC 1.10106(T) = NBRC 109639(T)).

Arcticibacter pallidicorallinus sp. nov. isolated from glacier ice.

PubMed

Liu, Qing; Kim, Song-gun; Liu, Hong-can; Xin, Yu-hua; Zhou, Yu-guang

2014-07-01

A Gram-stain-negative, rod-shaped bacterium (strain Hh36(T)) was isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh36(T) were pink, convex and round on PYG medium plates. Strain Hh36(T) was able to grow at 4-30 °C and pH 6.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh36(T) was related to members of the genus Arcticibacter. The major cellular fatty acids of the novel strain were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The G+C content of the genomic DNA was 44.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain Hh36(T) is considered to represent a novel species of the genus Arcticibacter, for which the name Arcticibacter pallidicorallinus sp. nov. is proposed. The type strain is Hh36(T) ( = CGMCC 1.9313(T)  = KCTC 32542(T)). © 2014 Institute of Microbiology, Chinese Academy of Sciences.

Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

PubMed

Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

2015-07-01

A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)).

The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

PubMed Central

Parker, Michael S.; Balasubramaniam, Ambikaipakan; Sallee, Floyd R.; Parker, Steven L.

2018-01-01

Eukaryote ribosomal RNAs (rRNAs) have expanded in the course of phylogeny by addition of nucleotides in specific insertion areas, the expansion segments. These number about 40 in the larger (25–28S) rRNA (up to 2,400 nucleotides), and about 12 in the smaller (18S) rRNA (<700 nucleotides). Expansion of the larger rRNA shows a clear phylogenetic increase, with a dramatic rise in mammals and especially in hominids. Substantial portions of expansion segments in this RNA are not bound to ribosomal proteins, and may engage extraneous interactants, including messenger RNAs (mRNAs). Studies on the ribosome-mRNA interaction have focused on proteins of the smaller ribosomal subunit, with some examination of 18S rRNA. However, the expansion segments of human 28S rRNA show much higher density and numbers of mRNA matches than those of 18S rRNA, and also a higher density and match numbers than its own core parts. We have studied that with frequent and potentially stable matches containing 7–15 nucleotides. The expansion segments of 28S rRNA average more than 50 matches per mRNA even assuming only 5% of their sequence as available for such interaction. Large expansion segments 7, 15, and 27 of 28S rRNA also have copious long (≥10-nucleotide) matches to most human mRNAs, with frequencies much higher than in other 28S rRNA parts. Expansion segments 7 and 27 and especially segment 15 of 28S rRNA show large size increase in mammals compared to other metazoans, which could reflect a gain of function related to interaction with non-ribosomal partners. The 28S rRNA expansion segment 15 shows very high increments in size, guanosine, and cytidine nucleotide content and mRNA matching in mammals, and especially in hominids. With these segments (but not with other 28S rRNA or any 18S rRNA expansion segments) the density and number of matches are much higher in 5′-terminal than in 3′-terminal untranslated mRNA regions, which may relate to mRNA mobilization via 5′ termini. Matches in the expansion segments 7, 15, and 27 of human 28S rRNA appear as candidates for general interaction with mRNAs, especially those associated with intracellular matrices such as the endoplasmic reticulum. PMID:29563925

Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.

PubMed

Watanabe, Tomohiro; Kojima, Hisaya; Shinohara, Arisa; Fukui, Manabu

2016-01-01

A novel sulfur-oxidizing bacterium, designated strain BiS0T, was isolated from a sediment sample collected from a freshwater lake in Japan. The cells were rod-shaped, 1.4-4.6 × 0.4-0.7 μm and Gram-stain-negative. The G+C content of the genomic DNA was around 44 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C10 : 0 3-OH as major cellular fatty acids. Strain BiS0T grew by carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as the electron acceptor. Growth was observed over a temperature range of 0-32 °C (optimum, 15-22 °C), an NaCl concentration range of 0-546.4 mM (optimum 0-66.7 mM) and a pH range of 5.2-8.1 (optimum 6.1-6.3). Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BiS0T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relatives were Sulfuricella denitrificans skB26T and Sulfuricella sp. T08, with 16S rRNA gene sequence similarities of 96.3 %. On the basis of the data obtained in this study, strain BiS0T represents a novel species of a novel genus, for which the name Sulfurirhabdus autotrophica gen. nov., sp. nov. is proposed. The type strain is BiS0T ( = NBRC 110941T = DSM 100309T).

Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella.

PubMed

Abraham, Wolf-Rainer; de Carvalho, Maira Peres; da Costa Neves, Thais Souto Paula; Memoria, Marina Torquato; Tartuci, Iago Toledo; Vancanneyt, Marc; Smit, John; Rohde, Manfred

2017-08-01

Two Gram-negative, heterotrophic, aerobic, prosthecated, marine bacteria, designated strains MCS23T and MCS27T, were isolated from seawater samples. NaCl was required for growth. The major polar lipid detected in strain MCS27T was phosphatidylglycerol, whereas those detected in MCS23T were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and 1,2-diacyl-3-α-d-glucuronopyranosyl-sn-glycerol taurineamide. The most abundant cellular fatty acids were C18 : 1ω7 and C16 : 0, hydroxyl-fatty acids were 3-OH C12 : 0 in both strains and 3-OH C11 : 0 in MCS23T. Strains MCS23T and MCS27T had DNA G+C contents of 57.0 and 55.0 mol%, respectively. The two strains shared 99.3 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Henriciella were 99.4-97.8 % but DNA-DNA hybridizations were 53 % or lower. Besides their 16S rRNA gene sequences, the novel strains can be differentiated from other species of the genus Henriciella by cell morphology, lipid and fatty acid patterns and enzyme activities. The data obtained led to the identification of two novel species, for which the names Henriciella barbarensis sp. nov. (type strain MCS23T=LMG 28705T=CCUG 66934T) and Henriciella algicola sp. nov. (type strain MCS27T=LMG 29152T=CCUG 67844T) are proposed. As these two novel species are the first prosthecate species in the genus Henriciella, an emended genus description is also provided.

Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.

PubMed

Xu, Yongle; Zhang, Rui; Li, Qipei; Liu, Keshao; Jiao, Nianzhi

2015-02-01

A novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000(T), was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T: were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000(T) was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000(T) formed a branch within the genus Marivirga, but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea. The 16S rRNA gene sequence similarity of strain JLT2000(T) with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000(T) had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). In addition, strain JLT2000(T) could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). Based on this polyphasic analysis, strain JLT2000(T) represents a novel species of the genus Marivirga, for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000(T) ( = JCM 18012(T) = CGMCC 1.10832(T)). © 2015 IUMS.

Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea.

PubMed

Lucena, Teresa; Ruvira, María A; Macián, M Carmen; Pujalte, María J; Arahal, David R

2014-04-01

Strain 4SM10(T), an aerobic marine, Gram-negative, heterotrophic and non pigmented bacterium isolated from seawater from Vinaroz in Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence placed the strain within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analyses also showed that strain 4SM10(T) forms a stable clade with species of the genus Roseovarius, being related to Roseovarius nubinhibens ISM(T) and Roseovarius aestuarii SMK-122(T) at 97.5 and 97.4 % 16S rRNA sequence similarity, respectively. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strain 4SM10(T) does not belong to the same species as R. aestuarii CECT 7745(T) and Roseovarius nubinhibens CECT 7750(T) displaying ANI values well below the 95 % boundary for genomic species. Strain 4SM10(T) requires Na(+) plus a divalent cation (either Mg(2+) or Ca(2+)) to grow, reduces nitrate to nitrite and uses a large number of amino acids and organic acids (but no carbohydrates) as sole carbon sources. Enzymatic activities displayed in API ZYM tests are alkaline phosphatase, leucine arylamidase and acid phosphatase. The major cellular fatty acids were identified as C18:1 ω7c and/or C18:1 ω6c (67.1 %). The DNA G+C content was determined to be 54.27 mol%. Based on the genotypic and phenotypic data obtained, the name Roseovarius albus sp. nov. is proposed for this novel taxon, with the type strain 4SM10(T) (=CECT 7450(T) = KCTC 22653(T)).

Marinagarivorans algicola gen. nov., sp. nov., isolated from marine algae.

PubMed

Guo, Ling-Yun; Li, Dong-Qi; Sang, Jin; Chen, Guan-Jun; Du, Zong-Jun

2016-03-01

Two novel agar-degrading, Gram-stain-negative, motile, heterotrophic, facultatively anaerobic and pale yellow-pigmented bacterial strains, designated Z1 T and JL1, were isolated from marine algae Gelidium amansii (Lamouroux) and Gracilaria verrucosa , respectively. Growth of the isolates was optimal at 28-30 °C, pH 7.0-7.5 and with 2-3 % (w/v) NaCl. Both strains contained Q-8 as the sole respiratory quinone. The major cellular fatty acids in strain Z1 T were C 18 : 1 ω7 c , C 16 : 0 and summed feature 3 (C 16 : 1 ω7 c and/or iso-C 15 : 0 2-OH). The predominant polar lipids in strain Z1 T were phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The genomic DNA G+C content of both strains was 45.1 mol%. Strains Z1 T and JL1 were closely related, with 99.9 % 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) value between strains Z1 T and JL1 was 99.3 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains Z1 T and JL1 form a distinct phyletic line within the class Gammaproteobacteria , with less than 92.3 % similarity to their closest relatives. Based on data from the current polyphasic study, the isolates are proposed to belong to a novel species of a new genus designated Marinagarivorans algicola gen. nov., sp. nov. The type strain of the type species is Z1 T ( = ATCC BAA-2617 T  = CICC 10859 T ).

Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae.

PubMed

Zhou, En-Min; Yu, Tian-Tian; Liu, Lan; Ming, Hong; Yin, Yi-Rui; Dong, Lei; Tseng, Min; Nie, Guo-Xing; Li, Wen-Jun

2014-09-01

Strains YIM 77562(T) and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50-55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family Thermoactinomycetaceae. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the Thermoactinomycetaceae were 88.33-93.24 %; the highest sequence similarity was with Hazenella coriacea DSM 45707(T). In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562(T) and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA-DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562(T) ( = CCTCC AA 2011022(T) = JCM 18057(T)). © 2014 IUMS.

Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden.

PubMed

Huq, Md Amdadul

2018-03-01

A novel bacterial strain MAH-8 T was isolated from a soil sample of a Korean pine garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, pinkish yellow colored, motile and vibrio-shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28-30 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-8 T belongs to the genus Caenispirillum and is most closely related to Caenispirillum bisanense KCTC 12839 T (98.14%), Caenispirillum deserti KCTC 42064 T (96.35%), and Caenispirillum salinarum JCM 17360 T (95.76%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-8 T and its closest phylogenetic neighbor was below 45.0%. The DNA G + C content was 70.5 mol% and the predominant respiratory quinone was ubiquinone-10. Flexirubin-type pigments were present and the major cellular fatty acids were C 18:1 ω7c/C 18:1 ω6c, C 16:1 ω7c/C 16:1 ω6c and C 16:0 . The results of DNA-DNA hybridization and genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-8 T represented a novel species within the genus Caenispirillum, for which the name Caenispirillum humi, is proposed. The type strain is MAH-8 T (= KACC 19294 T  = CGMCC 1.16224 T ). The NCBI GenBank Accession Number for the 16S rRNA gene sequence of strain MAH-8 T is KY964275.

Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.

PubMed

Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

2014-11-01

A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10% (w/v) and optimal growth was achieved at 3% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C(18 : 1)ω7c, C(16:0) and C(17 : 0), and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81% and 2%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) ( = IBRC-M 10765(T) =CECT 8342(T)). © 2014 IUMS.

Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil.

PubMed

Jiang, Fan; Danzeng, Wangmu; Zhang, Yuming; Zhang, Yan; Jiang, Li; Liu, Jia; Lu, Lu; Fan, Wei; Peng, Fang

2018-02-01

A red-pigmented, Gram-reaction-negative, aerobic, non-motile and rod-shaped bacterium, designated NY03-3-30 T , was isolated from a soil sample collected from Inexpressible Island, Northern Victoria Land of the Antarctic Ross Orogen, and subjected to a polyphasic taxonomic study. Growth occurred at 4-28 °C (optimum 20 °C) and at pH 6.0-9.0 (optimum pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NY03-3-30 T belonged to the genus Hymenobacter in the family Cytophagaceae. 16S rRNA gene sequence similarities between strain NY03-3-30 T and the type strains of Hymenobacter species with validly published names ranged from 92.7 to 96.2 %. Strain NY03-3-30 T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 0, C16 : 1ω5c, anteiso-C15 : 0 and summed feature 4 (iso-C17 : 1-I and/or anteiso-C17 : 1-B) as major cellular fatty acids, MK-7 as the respiratory quinone and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain NY03-3-30 T was 59.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain NY03-3-30 T is considered to represent a novel species of genus Hymenobacter, for which the name Hymenobacter rubripertinctus sp. nov. is proposed. The type strain is NY03-3-30 T (=CCTCC AB 2017095 T =KCTC 62163 T ).

Luteolibacter arcticus sp. nov., isolated from high Arctic tundra soil, and emended description of the genus Luteolibacter.

PubMed

Kim, MyongChol; Pak, SeHong; Rim, SongGuk; Ren, Lvzhi; Jiang, Fan; Chang, Xulu; Liu, Ping; Zhang, Yumin; Fang, Chengxiang; Zheng, Congyi; Peng, Fang

2015-06-01

A pale yellow, Gram-reaction-negative, non-motile, aerobic bacterium, designated MC 3726T, was isolated from a tundra soil near Ny-Ålesund, Svalbard Archipelago, Norway (78 °N). Growth occurred at 4-37 °C (optimum 25-30 °C) and at pH 5.0-9.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MC 3726T belonged to the genus Luteolibacter in the family Verrucomicrobiaceae. The 16S rRNA gene sequence of this strain showed 93.18, 92.54 and 92.44 % similarity to those of Luteolibacter cuticulihirudinis E100T, Luteolibacter pohnpeiensis A4T-83T and Luteolibacter yonseiensis EBTL01T, respectively. The cell wall of strain MC 3726T contained meso-diaminopimelic acid as the diagnostic amino acid. Strain MC 3726T contained iso-C14:0 (38.28 %), C16:0 (15.89 %), C16:1ω9c (14.24 %), iso-C16:0 (10.42 %) and anteiso-C15:0 (5.75 %) as the predominant cellular fatty acids, MK-9 and MK-10 as the major respiratory quinones, and phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the main polar lipids. The DNA G+C content was 60.7 mol %. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MC 3726T is considered to represent a novel species of the genus Luteolibacter, for which the name Luteolibacter arcticus sp. nov. is proposed. The type strain is MC 3726T ( = CCTCC AB 2014275T = LMG 28638T). An emended description of the genus Luteolibacter is also provided, along with emended descriptions of Luteolibacter cuticulihirudinis, Luteolibacter yonseiensis and Luteolibacter pohnpeiensis.

Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough.

PubMed

Toffin, Laurent; Zink, Klaus; Kato, Chiaki; Pignet, Patricia; Bidault, Adeline; Bienvenu, Nadège; Birrien, Jean-Louis; Prieur, Daniel

2005-01-01

A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at pH 7.0 was 4-50 degrees C, with the optimum at 37-40 degrees C. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2(T) (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).

Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr].

PubMed

Li, Zhilei; Song, Wei; Zhao, Junwei; Zhuang, Xiaoxin; Zhao, Yue; Wang, Xiangjing; Xiang, Wensheng

2017-12-01

A novel actinomycete, designated strain NEAU-BB2C19 T , was isolated from the root of black soya bean [Glycine max (L.) Merr] collected from Harbin, Heilongjiang Province, China, and characterized using a polyphasic approach. The strain was an aerobic, Gram-stain-positive actinomycete that formed extensively branched substrate mycelium and aerial hyphae. The predominant menaquinones were MK-9(H2) and MK-9(H0). The major cellular fatty acid profile consisted of iso-C16 : 0, 10-methyl C17 : 0 and 10-methyl C18 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylglycerol and glycolipid. The DNA G+C content was 68.2±0.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-BB2C19 T should be assigned to the genus Nonomuraea and formed a distinct branch with its closest neighbour Nonomuraea guangzhouensis NEAU-ZJ3 T (98.75 % 16S rRNA gene sequence similarity). The morphological and chemotaxonomic properties of the strain were also consistent with those of members of the genus Nonomuraea. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-BB2C19 T could be clearly differentiated from its closest phylogenetic relative. Thus, the strain is concluded to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea glycinis sp. nov. is proposed. The type strain is NEAU-BB2C19 T (=CGMCC 4.7430 T =DSM 104838 T ).

Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera.

PubMed

Kim, Pil Soo; Shin, Na-Ri; Kim, Joon Yong; Yun, Ji-Hyun; Hyun, Dong-Wook; Bae, Jin-Woo

2014-08-01

A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18(T), was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidase-negative and catalase-positive. Strain HYN18(T) showed optimum growth at 25°C, pH 6-7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18(T) was most closely related to Acinetobacter nectaris SAP 763.2(T) and A. boissieri SAP 284.1(T) with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2(T) (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c /C16:1ω6c ), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain HYN18(T) were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNA-DNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2(T). Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18(T) is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18(T) (=KACC 16906(T) =JCM 18575(T)).

Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil.

PubMed

Xu, Lian; Sun, Ji-Quan; Wang, Li-Juan; Gao, Zhi-Wei; Sun, Li-Zhu; Wu, Xiao-Lei

2017-06-01

A Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14T was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14T could grow at 10-40 °C (optimally at 30 °C), pH 6.0-10.0 (optimally at pH 8.0), and in the presence of 0-6.0 % (w/v) NaCl (optimally with 0-2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B (gyrB) gene sequences revealed that strain Y3L14T clustered with strains belonging to the genus Sphingobacterium, sharing the highest 16S rRNA gene sequence similarity with Sphingobacterium lactis WCC 4512T (94.99 %). Its major cellular fatty acids contained iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14T contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14T was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14T represents a novel species within the genus Sphingobacterium, for which Sphingobacterium alkalisoli sp. nov. is proposed; the type strain is Y3L14T (=CGMCC 1.15782T=KCTC 52379T).

Streptomyces ovatisporus sp. nov., isolated from deep marine sediment.

PubMed

Veyisoglu, Aysel; Cetin, Demet; Inan Bektas, Kadriye; Guven, Kiymet; Sahin, Nevzat

2016-11-01

The taxonomic position of a Gram-staining-positive strain, designated strain S4702T was isolated from a marine sediment collected from the southern Black Sea coast, Turkey, determined using a polyphasic approach. The isolate was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its classification as representing a member of the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree. S4702T was found to be most closely related to the type strains of Streptomyces marinus(DSM 41968T; 97.8 % sequence similarity) and Streptomyces abyssalis (YIM M 10400T; 97.6 %). 16S rRNA gene sequence similarities with other members of the genus Streptomyces were lower than 97.5 %. DNA-DNA relatedness of S4702T and the most closely related strain S. marinus DSM 41968T was 21.0 %. The G+C content of the genomic DNA was 72.5 mol%. The cell wall of the strain contained l,l-diaminopimelic acid and the cell-wall sugars were glucose and ribose. The major cellular fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H8). The polar lipid profile of S4702T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. S4702T could be distinguished from its closest phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that S4702T represents a novel species of the genus Streptomyces, for which the name Streptomyces ovatisporus sp. nov. is proposed. The type strain is S4702T (DSM 42103T=KCTC 29206T=CGMCC 4.7357T).

Bacillus kyonggiensis sp. nov., isolated from soil of a lettuce field.

PubMed

Dong, Ke; Lee, Sangseob

2011-10-01

A Gram-positive, rod-shaped, motile, endospore-forming bacterial strain, designated NB22(T), was isolated from soil of a lettuce field in Kyonggi province, South Korea, and was characterized by using a polyphasic taxonomic approach. This novel isolate grew optimally at 30-37°C and pH 8-9. It grew in the presence of 0-4% NaCl (optimum, 1-2%). Comparative 16S rRNA gene sequence analysis showed that strain NB22(T) was closely related to members of the genus Bacillus and fell within a coherent cluster comprising B. siralis 171544(T) (98.1%) and B. korlensis ZLC-26(T) (97.3%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.4%. Strain NB22(T) had a genomic DNA G+C content of 36.3 mol% and the predominant respiratory quinone was MK-7. The peptidoglycan contained meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15:0), anteiso-C(15:0), C(14:0), and C(16:0). These chemotaxonomic results supported the affiliation of strain NB22(T) to the genus Bacillus, and the low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain NB22(T) from recognized Bacillus species. On the basis of the evidence presented, strain NB22(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus kyonggiensis sp. nov. is proposed. The type strain is NB22(T) (=KEMB 5401-267(T) =JCM 17569(T)).

Hymenobacter arcticus sp. nov., isolated from glacial till.

PubMed

Chang, Xulu; Zheng, Jiangli; Jiang, Fan; Liu, Ping; Kan, Wenjing; Qu, Zhihao; Fang, Chengxiang; Peng, Fang

2014-06-01

A novel, red-pink-pigmented strain, designated R2-4(T), was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4-30 °C (optimum, 20-22 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-1% NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4(T) belonged to the genus Hymenobacter. 16S rRNA gene sequence similarity between strain R2-4(T) and the type strains of related species of the genus ranged from 94.51 to 96.05%. Strain R2-4(T) contained iso-C(15 : 0), anteiso-C(15 : 0), summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c), summed feature 4 (C(17 : 1) anteiso B and/or iso I) and C(16 : 1)ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4(T) was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4(T) is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4(T) ( = CCTCC AB 2012104(T) = KACC 16881(T)). © 2014 IUMS.

Microvirga soli sp. nov., an alphaproteobacterium isolated from soil.

PubMed

Dahal, Ram Hari; Kim, Jaisoo

2017-01-01

An aerobic, Gram-stain-negative, catalase-positive and oxidase-negative, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium designated strain R491T was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R491T formed a lineage within the family Methylobacteriaceae of the phylum Proteobacteria that was distinct from various species of the genus Microvirga, including Microvirgaaerilata 5420S-16T (97.83 % 16S rRNA gene sequence similarity), Microvirga zambiensis WSM3693T (97.76 %), Microvirga flocculans ATCC BAA-817T (97.41 %), and Microvirga lupini Lut6T, Microvirga subterranea DSM 14364T, Microvirga vignae BR3299T, and Microvirga guangxiensis 25BT (96.99 %). The major polar lipids of strain R491T were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 71.2 %), C16 : 0 (12.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.7 %), and C18 : 0 (4.2 %). The DNA G+C content of strain R491T was 61.8 mol%. DNA-DNA hybridization values between strain R491T and other members of the genus Microvirga ranged from 27 to 57 %. On the basis of phenotypic, genotypic and phylogenetic analyses, strain R491T represents a novel species of the genus Microvirga, for which the name Microvirga soli sp. nov. is proposed. The type strain is R491T (=KEMB 9005-408T=KACC 18969T=NBRC 112417T).

Key Markers of mTORC1-Dependent and mTORC1-Independent Signaling Pathways Regulating Protein Synthesis in Rat Soleus Muscle During Early Stages of Hindlimb Unloading.

PubMed

Mirzoev, Timur; Tyganov, Sergey; Vilchinskaya, Natalia; Lomonosova, Yulia; Shenkman, Boris

2016-01-01

The purpose of the study was to assess the amount of rRNA and phosphorylation status of the key markers of mTORC1-dependent (70s6k, 4E-BP1) and mTORC1-independent (GSK-3β, AMPK) signaling pathways controlling protein synthesis in rat soleus during early stages of mechanical unloading (hindlimb suspension (HS) for 1-, 3- and 7 days). The content of the key signaling molecules of various anabolic signaling pathways was determined by Western-blotting. The amount of 28S rRNA was evaluated by RT-PCR. The rate of protein synthesis was assessed using in-vivo SUnSET technique. HS for 3 and 7 days induced a significant (p<0.05) decrease in the rate of global protein synthesis in soleus muscle in comparison with control. HS within 24 hours resulted in a significant (p<0.05) decrease in p-4E-BP1 content, p-AMPK content and increase in p-p70s6k content in rat soleus muscle. Following three days of HS the content of p-AKT was decreased (p<0.05). After 7 days of HS the phosphorylation level of AKT and GSK-3beta was significantly reduced (p<0.05) compared to control. We also observed a significant decrease in the amount of 28S rRNA in rat soleus following 1, 3 and 7 days of HS. Taken together, the results of our study suggest that a decline in the global rate of protein synthesis in rat soleus during early stages of simulated microgravity is associated with impaired ribosome biogenesis as well as reduced activity of mTORC1-independent signaling pathways. © 2016 The Author(s) Published by S. Karger AG, Basel.

5SRNAdb: an information resource for 5S ribosomal RNAs.

PubMed

Szymanski, Maciej; Zielezinski, Andrzej; Barciszewski, Jan; Erdmann, Volker A; Karlowski, Wojciech M

2016-01-04

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number

PubMed Central

Tadmor, Arbel D.; Tlusty, Tsvi

2008-01-01

We propose a biophysical model of Escherichia coli that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity. PMID:18437222

Phenotypic and phylogenetic characterization of ruminal tannin-tolerant bacteria.

PubMed

Nelson, K E; Thonney, M L; Woolston, T K; Zinder, S H; Pell, A N

1998-10-01

The 16S rRNA sequences and selected phenotypic characteristics were determined for six recently isolated bacteria that can tolerate high levels of hydrolyzable and condensed tannins. Bacteria were isolated from the ruminal contents of animals in different geographic locations, including Sardinian sheep (Ovis aries), Honduran and Colombian goats (Capra hircus), white-tail deer (Odocoileus virginianus) from upstate New York, and Rocky Mountain elk (Cervus elaphus nelsoni) from Oregon. Nearly complete sequences of the small-subunit rRNA genes, which were obtained by PCR amplification, cloning, and sequencing, were used for phylogenetic characterization. Comparisons of the 16S rRNA of the six isolates showed that four of the isolates were members of the genus Streptococcus and were most closely related to ruminal strains of Streptococcus bovis and the recently described organism Streptococcus gallolyticus. One of the other isolates, a gram-positive rod, clustered with the clostridia in the low-G+C-content group of gram-positive bacteria. The sixth isolate, a gram-negative rod, was a member of the family Enterobacteriaceae in the gamma subdivision of the class Proteobacteria. None of the 16S rRNA sequences of the tannin-tolerant bacteria examined was identical to the sequence of any previously described microorganism or to the sequence of any of the other organisms examined in this study. Three phylogenetically distinct groups of ruminal bacteria were isolated from four species of ruminants in Europe, North America, and South America. The presence of tannin-tolerant bacteria is not restricted by climate, geography, or host animal, although attempts to isolate tannin-tolerant bacteria from cows on low-tannin diets failed.

Phenotypic and Phylogenetic Characterization of Ruminal Tannin-Tolerant Bacteria

PubMed Central

Nelson, Karen E.; Thonney, Michael L.; Woolston, Tina K.; Zinder, Stephen H.; Pell, Alice N.

1998-01-01

The 16S rRNA sequences and selected phenotypic characteristics were determined for six recently isolated bacteria that can tolerate high levels of hydrolyzable and condensed tannins. Bacteria were isolated from the ruminal contents of animals in different geographic locations, including Sardinian sheep (Ovis aries), Honduran and Colombian goats (Capra hircus), white-tail deer (Odocoileus virginianus) from upstate New York, and Rocky Mountain elk (Cervus elaphus nelsoni) from Oregon. Nearly complete sequences of the small-subunit rRNA genes, which were obtained by PCR amplification, cloning, and sequencing, were used for phylogenetic characterization. Comparisons of the 16S rRNA of the six isolates showed that four of the isolates were members of the genus Streptococcus and were most closely related to ruminal strains of Streptococcus bovis and the recently described organism Streptococcus gallolyticus. One of the other isolates, a gram-positive rod, clustered with the clostridia in the low-G+C-content group of gram-positive bacteria. The sixth isolate, a gram-negative rod, was a member of the family Enterobacteriaceae in the gamma subdivision of the class Proteobacteria. None of the 16S rRNA sequences of the tannin-tolerant bacteria examined was identical to the sequence of any previously described microorganism or to the sequence of any of the other organisms examined in this study. Three phylogenetically distinct groups of ruminal bacteria were isolated from four species of ruminants in Europe, North America, and South America. The presence of tannin-tolerant bacteria is not restricted by climate, geography, or host animal, although attempts to isolate tannin-tolerant bacteria from cows on low-tannin diets failed. PMID:9758806

Genome-wide gene order distances support clustering the gram-positive bacteria

PubMed Central

House, Christopher H.; Pellegrini, Matteo; Fitz-Gibbon, Sorel T.

2015-01-01

Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D′ = −ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R2 = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R2 = 0.52). Gene content is only weakly correlated with rRNA divergence (R2 = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R2 = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell. PMID:25653643

RINT-1 interacts with MSP58 within nucleoli and plays a role in ribosomal gene transcription.

PubMed

Yang, Chuan-Pin; Kuo, Yu-Liang; Lee, Yi-Chao; Lee, Kuen-Haur; Chiang, Chi-Wu; Wang, Ju-Ming; Hsu, Che-Chia; Chang, Wen-Chang; Lin, Ding-Yen

2016-09-16

The nucleolus is the cellular site of ribosomal (r)DNA transcription and ribosome biogenesis. The 58-kDa microspherule protein (MSP58) is a nucleolar protein involved in rDNA transcription and cell proliferation. However, regulation of MSP58-mediated rDNA transcription remains unknown. Using a yeast two-hybrid system with MSP58 as bait, we isolated complementary (c)DNA encoding Rad50-interacting protein 1 (RINT-1), as a MSP58-binding protein. RINT-1 was implicated in the cell cycle checkpoint, membrane trafficking, Golgi apparatus and centrosome dynamic integrity, and telomere length control. Both in vitro and in vivo interaction assays showed that MSP58 directly interacts with RINT-1. Interestingly, microscopic studies revealed the co-localization of MSP58, RINT-1, and the upstream binding factor (UBF), a rRNA transcription factor, in the nucleolus. We showed that ectopic expression of MSP58 or RINT-1 resulted in decreased rRNA expression and rDNA promoter activity, whereas knockdown of MSP58 or RINT-1 by siRNA exerted the opposite effect. Coexpression of MSP58 and RINT-1 robustly decreased rRNA synthesis compared to overexpression of either protein alone, whereas depletion of RINT-1 from MSP58-transfected cells enhanced rRNA synthesis. We also found that MSP58, RINT-1, and the UBF were associated with the rDNA promoter using a chromatin immunoprecipitation assay. Because aberrant ribosome biogenesis contributes to neoplastic transformation, our results revealed a novel protein complex involved in the regulation of rRNA gene expression, suggesting a role for MSP58 and RINT-1 in cancer development. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic nematode, Rotylenchulus reniformis.

PubMed

Nyaku, Seloame T; Sripathi, Venkateswara R; Kantety, Ramesh V; Gu, Yong Q; Lawrence, Kathy; Sharma, Govind C

2013-01-01

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene.

Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

PubMed Central

Nyaku, Seloame T.; Sripathi, Venkateswara R.; Kantety, Ramesh V.; Gu, Yong Q.; Lawrence, Kathy; Sharma, Govind C.

2013-01-01

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene. PMID:23593343

Common 5S rRNA variants are likely to be accepted in many sequence contexts

NASA Technical Reports Server (NTRS)

Zhang, Zhengdong; D'Souza, Lisa M.; Lee, Youn-Hyung; Fox, George E.

2003-01-01

Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The results demonstrate that changes that occur multiple times in a local region of RNA sequence space in fact usually will be accepted in any sequence context in that same local region.

Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning.

PubMed

Zhao, Zhongliang; Dammert, Marcel A; Hoppe, Sven; Bierhoff, Holger; Grummt, Ingrid

2016-09-30

Attenuation of ribosome biogenesis in suboptimal growth environments is crucial for cellular homeostasis and genetic integrity. Here, we show that shutdown of rRNA synthesis in response to elevated temperature is brought about by mechanisms that target both the RNA polymerase I (Pol I) transcription machinery and the epigenetic signature of the rDNA promoter. Upon heat shock, the basal transcription factor TIF-IA is inactivated by inhibition of CK2-dependent phosphorylations at Ser170/172. Attenuation of pre-rRNA synthesis in response to heat stress is accompanied by upregulation of PAPAS, a long non-coding RNA (lncRNA) that is transcribed in antisense orientation to pre-rRNA. PAPAS interacts with CHD4, the adenosine triphosphatase subunit of NuRD, leading to deacetylation of histones and movement of the promoter-bound nucleosome into a position that is refractory to transcription initiation. The results exemplify how stress-induced inactivation of TIF-IA and lncRNA-dependent changes of chromatin structure ensure repression of rRNA synthesis in response to thermo-stress. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Enhanced NOLC1 promotes cell senescence and represses hepatocellular carcinoma cell proliferation by disturbing the organization of nucleolus.

PubMed

Yuan, Fuwen; Zhang, Yu; Ma, Liwei; Cheng, Qian; Li, Guodong; Tong, Tanjun

2017-08-01

The nucleolus is a key organelle that is responsible for the synthesis of rRNA and assembly of ribosomal subunits, which is also the center of metabolic control because of the critical role of ribosomes in protein synthesis. Perturbations of rRNA biogenesis are closely related to cell senescence and tumor progression; however, the underlying molecular mechanisms are not well understood. Here, we report that cellular senescence-inhibited gene (CSIG) knockdown up-regulated NOLC1 by stabilizing the 5'UTR of NOLC1 mRNA, and elevated NOLC1 induced the retention of NOG1 in the nucleolus, which is responsible for rRNA processing. Besides, the expression of NOLC1 was negatively correlated with CSIG in the aged mouse tissue and replicative senescent 2BS cells, and the down-regulation of NOLC1 could rescue CSIG knockdown-induced 2BS senescence. Additionally, NOLC1 expression was decreased in human hepatocellular carcinoma (HCC) tissue, and the ectopic expression of NOLC1 repressed the proliferation of HCC cells and tumor growth in a HCC xenograft model. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Use of 16S-23S rRNA spacer-region (SR)-PCR for identification of intestinal clostridia.

PubMed

Song, Yuli; Liu, Chengxu; Molitoris, Denise; Tomzynski, Thomas J; Mc Teague, Maureen; Read, Erik; Finegold, Sydney M

2002-12-01

The suitability of a species identification technique based on PCR analysis of 16S-23S rRNA spacer region (SR) polymorphism for human intestinal Clostridium species was evaluated. This SR-PCR based technique is highly reproducible and successfully differentiated the strains tested, which included 17 ATCC type strains of Clostridium and 152 human stool Clostridium isolates, at the species or intraspecies level. Ninety-eight of 152 stool isolates, including C. bifermentans, C. butyricum, C. cadaveris, C. orbiscindens, C. paraputrificum, C. pefringens, C. ramosum, C. scindens, C. spiroforme, C. symbiosum and C. tertium, were identified to species level by SR-PCR patterns that were identical to those of their corresponding ATCC type strains. The other 54 stool isolates distributed among ten SR-PCR patterns that are unique and possibly represent ten novel Clostridium species or subspecies. The species identification obtained by SR-PCR pattern analysis completely agreed with that obtained by 16S rRNA sequencing, and led to identification that clearly differed from that obtained by cellular fatty acid analysis for 23/152 strains (15%). These results indicate that SR-PCR provides an accurate and rapid molecular method for the identification of human intestinal Clostridium species.

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

PubMed Central

Wüst, Pia K.; Nacke, Heiko; Kaiser, Kristin; Marhan, Sven; Sikorski, Johannes; Kandeler, Ellen; Daniel, Rolf

2016-01-01

Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actinobacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. PMID:26896137

Nucleotides in 16S rRNA that are required in unmodified form for features recognized by ribosomal protein S8.

PubMed Central

Thurlow, D L; Ehresmann, C; Ehresmann, B

1983-01-01

Nucleotides in 16S rRNA which are required in unmodified form for specific recognition of ribosomal protein S8 from Escherichia coli were identified using a damage-selection experimental approach. Prior to complex formation with S8, 16S rRNA was treated under fully denaturing conditions with either diethyl pyrocarbonate or 25% hydrazine. Following separation of bound from unbound fragments of RNA, those associated with S8 were analyzed for their content of modified bases by treatment with aniline. Nucleotides found to be consistently unmodified in such fragments were located near the base of a stable helix (encompassing bases 581-656) or near the apex of the helix on the 3' proximal side. A minor S8 ribonucleoprotein particle was found to contain fragments which extended in the 3' direction to position 671. Images PMID:6356037

Tepidimonas arfidensis Sp. Nov., a Novel Gram-negative and thermophilic bacterium isolated from the bone marrow of a patient with leukemia in Korea.

PubMed

Ko, Kwan Soo; Lee, Nam Yong; Oh, Won Sup; Lee, Jang Ho; Ki, Hyun Kyun; Peck, Kyong Ran; Song, Jae-Hoon

2005-01-01

A Gram-negative bacillus, SMC-6271(T), which was isolated from the bone marrow of a patient with leukemia but could not be identified by a conventional microbiologic method, was characterized by a genotypic analysis of 16S rRNA gene. Sequences of the 16S rRNA gene revealed that this bacterium was closely related to Tepidimonas ignava and other slightly thermophilic isolates but diverged distinctly from them. Analyses of cellular fatty acid composition and performance of biochemical tests confirmed that this bacterium is a distinct species from the other Tepidimonas species. Based on the evaluated phenotypic and genotypic characteristics, it is proposed that SMC-6271T (=ABB 0301T =KCTC 12412T =JCM 13232T) should be classified as a new species, namely Tepidimonas arfidensis sp. nov.

Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis.

PubMed

Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo

2012-02-24

Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.

Aromatic-degrading Sphingomonas isolates from the deep subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, J.K.; Romine, M.F.; Balkwill, D.L.

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1{omega}7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16SrRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequencemore » analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [{sup 14C}]toluene and [{sup 14C}]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobiolis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment. 41 refs., 2 figs., 5 tabs.« less

Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus.

PubMed

Klykleung, Nattaporn; Phongsopitanun, Wongsakorn; Pittayakhajonwut, Pattama; Ohkuma, Moriya; Kudo, Takuji; Tanasupawat, Somboon

2016-10-01

The novel endophytic actinomycete strain PA1-07T was isolated from the stem of Phyllanthus amarus. The strain displayed the consistent characteristics of members of the genus Streptomyces. The strain produced short spiral spore chains on aerial mycelia. It grew at pH 5-9, at 40 °C and with a maximum of 5 % (w/v) NaCl. It contained ll-diaminopimelic acid, glucose and ribose in the whole-cell hydrolysate. The major cellular menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), while the major cellular fatty acids were C16 : 0, iso-C14 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and four unknown lipids. The DNA G+C content of the strain was 71 mol%. The strain showed the highest 16S rRNA gene sequence similarity with Streptomyces curacoi JCM 4219T (98.77 %). The DNA-DNA relatedness values between strain PA1-07T and S. curacoi JCM 4219T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of these phenotypic and genotypic characteristics, the strain could be distinguished from closely related species of the genus Streptomyces and thus represents a novel species of the genus Streptomyces, for which the name Streptomyces phyllanthi sp. nov. is proposed. The type strain is PA1-07T (=JCM 30865T=KCTC 39785T=TISTR 2346T).

Nucleolar Targeting by Platinum: p53-Independent Apoptosis Follows rRNA Inhibition, Cell-Cycle Arrest, and DNA Compaction

PubMed Central

2015-01-01

TriplatinNC is a highly positively charged, substitution-inert derivative of the phase II clinical anticancer drug, BBR3464. Such substitution-inert complexes form a distinct subset of polynuclear platinum complexes (PPCs) interacting with DNA and other biomolecules through noncovalent interactions. Rapid cellular entry is facilitated via interaction with cell surface glycosoaminoglycans and is a mechanism unique to PPCs. Nanoscale secondary ion mass spectrometry (nanoSIMS) showed rapid distribution within cytoplasmic and nucleolar compartments, but not the nucleus. In this article, the downstream effects of nucleolar localization are described. In human colon carcinoma cells, HCT116, the production rate of 47S rRNA precursor transcripts was dramatically reduced as an early event after drug treatment. Transcriptional inhibition of rRNA was followed by a robust G1 arrest, and activation of apoptotic proteins caspase-8, -9, and -3 and PARP-1 in a p53-independent manner. Using cell synchronization and flow cytometry, it was determined that cells treated while in G1 arrest immediately, but cells treated in S or G2 successfully complete mitosis. Twenty-four hours after treatment, the majority of cells finally arrest in G1, but nearly one-third contained highly compacted DNA; a distinct biological feature that cannot be associated with mitosis, senescence, or apoptosis. This unique effect mirrored the efficient condensation of tRNA and DNA in cell-free systems. The combination of DNA compaction and apoptosis by TriplatinNC treatment conferred striking activity in platinum-resistant and/or p53 mutant or null cell lines. Taken together, our results support that the biological activity of TriplatinNC reflects reduced metabolic deactivation (substitution-inert compound not reactive to sulfur nucleophiles), high cellular accumulation, and novel consequences of high-affinity noncovalent DNA binding, producing a new profile and a further shift in the structure–activity paradigms for antitumor complexes. PMID:25407898

Identification of moderately halophilic bacteria from Thai fermented fish ( pla-ra ) and proposal of Virgibacillus siamensis sp. nov.

PubMed

Tanasupawat, Somboon; Chamroensaksri, Nitcha; Kudo, Takuji; Itoh, Takashi

2010-10-01

Forty-one isolates of moderately halophilic bacteria were isolated from fermented fish (pla-ra) in Thailand. On the basis of their phenotypic and chemotaxonomic characteristics, DNA-DNA relatedness and 16S rRNA gene sequences analyses, they were divided into six groups. The isolates in Group I to V were Gram-positive rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone with seven isoprene units (MK-7). An isolate in Group VI was a Gram-negative rod-shaped bacterium. The DNA G+C contents of tested strains ranged from 36.5-63 mol%. Ten strains (Group I) were identified as Virgibacillus dokdonensis, 13 isolates (Group II) as V. halodenitrificans, 14 isolates (Group III) as V. marismortui, 1 isolate (Group IV) as Virgibacillus sp., 2 isolates (Group V) as Bacillus vietnamnensis, and 1 isolate (Group VI) as Chromohalobacter salexigens. Isolate MS3-4 in Group IV was closely related to V. carmonensis KCTC 3819(T) (95.9%). This strain contained anteiso-C(15:0) (55.8%) and anteiso-C(17:0) (17.7%) as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as polar lipids. The DNA G+C content of MS3-4 was 38.0 mol%. The strain from Group IV is proposed as Virgibacillus siamensis sp. nov. and MS3-4(T) is the type strain (JCM 15395(T) =PCU 312(T) =TISTR 1957(T)).

Oceanobacillus kapialis sp. nov., from fermented shrimp paste in Thailand.

PubMed

Namwong, Sirilak; Tanasupawat, Somboon; Lee, Keun Chul; Lee, Jung-Sook

2009-09-01

A Gram-positive, rod-shaped, strictly aerobic, spore-forming, moderately halophilic bacterium, designated strain SSK2-2T, was isolated from fermented shrimp paste (ka-pi) produced in Thailand. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The isolate grew at 8-43 degrees C, pH 6-9 and in 0.5-24% (w/v) NaCl (optimum, 6-14% NaCl). The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. Phosphatidylglycerol and diphosphatidylglycerol were the major polar lipid components. The DNA G+C content was 39.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SSK2-2T was most closely related to Oceanobacillus picturae KCTC 3821T with 98.7% sequence similarity. Based on phenotypic and molecular features combined with DNA-DNA hybridization results (

Aminocella lysinolytica gen. nov., sp. nov., a L-lysine-degrading, strictly anaerobic bacterium in the class Clostridia isolated from a methanogenic reactor of cattle farms.

PubMed

Ueki, Atsuko; Shibuya, Toru; Kaku, Nobuo; Ueki, Katsuji

2015-01-01

A strictly anaerobic bacterial strain (WN037(T)) was isolated from a methanogenic reactor. Cells were Gram-positive rods. Strain WN037(T) was asaccharolytic. The strain fermented L-lysine in the presence of B-vitamin mixture or vitamin B12 and produced acetate and butyrate. L-arginine and casamino acids poorly supported the growth. Strain WN037(T) used neither other amino acids nor organic acids examined. The strain had C18:1 ω7c, C16:0 and C18:1 ω7c DMA as the predominant cellular fatty acids. The genomic DNA G + C content was 44.2 mol %. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain WN037(T) in the family Eubacteriaceae in the class Clostridia. The closest relative was Eubacterium pyruvativorans (sequence similarity, 92.8 %). Based on the comprehensive analyses, the novel genus and species, Aminocella lysinolytica gen. nov., sp. nov. was proposed to accommodate the strain. The type strain is WN037(T) (= JCM 19863(T) = DSM 28287(T)).

Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation.

PubMed

Kwon, Soon-Wo; Lee, Seon-Young; Kim, Byung-Yong; Weon, Hang-Yeon; Kim, Jung-Bong; Go, Seung-Joo; Lee, Gil-Bok

2007-08-01

A group of five bacilli, designated strains 4T12, 4T19(T), 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6-96.9 %) with respect to Bacillus herbersteinensis DSM 16534(T). The values for DNA-DNA hybridization (approx. 85-96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C(15 : 0) (approx. 24.5-33.9 %) and C(16 : 0) (approx. 15.1-34.1 %). The DNA G+C contents were 37.7-40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19(T) (=KACC 11279(T) =DSM 17723(T)).

Virgibacillus ainsalahensis sp. nov., a Moderately Halophilic Bacterium Isolated from Sediment of a Saline Lake in South of Algeria.

PubMed

Amziane, Meriam; Darenfed-Bouanane, Amel; Abderrahmani, Ahmed; Selama, Okba; Jouadi, Lydia; Cayol, Jean-Luc; Nateche, Farida; Fardeau, Marie-Laure

2017-02-01

A Gram-positive, moderately halophilic, endospore-forming bacterium, designated MerV T , was isolated from a sediment sample of a saline lake located in Ain Salah, south of Algeria. The cells were rod shaped and motile. Isolate MerV T grew at salinity interval of 0.5-25% NaCl (optimum, 5-10%), pH 6.0-12.0 (optimum, 8.0), and temperature between 10 and 40 °C (optimum, 30 °C).The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, a phospholipid, and two lipids, and MK-7 is the predominant menaquinone. The predominant cellular fatty acids were anteiso C 15:0 and anteiso C 17:0 . The DNA G+C content was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MerV T was most closely related to Virgibacillus halodenitrificans (gene sequence similarity of 97.0%). On the basis of phenotypic, chemotaxonomic properties, and phylogenetic analyses, strain MerV T (=DSM = 28944 T ) should be placed in the genus Virgibacillus as a novel species, for which the name Virgibacillus ainsalahensis is proposed.

Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae.

PubMed

Liu, Qian-Qian; Li, Xiao-Li; Rooney, Alejandro P; Du, Zong-Jun; Chen, Guan-Jun

2014-10-01

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22(T), was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33-35 °C, pH 7.0-7.5, and in the presence of 2-4% (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH and iso-C15:0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22(T) fell within the class Bacteroidia. Its closest phylogenetic neighbour was the recently described species Draconibacterium orientale, the sole member of the family Draconibacteriaceae, with merely 90.04% sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family Draconibacteriaceae. The type strain is G22(T) ( = CICC 10587(T) =DSM 27063(T)).

Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water.

PubMed

Wong, Shu-Kuan; Park, Sanghwa; Lee, Jung-Sook; Lee, Keun Chul; Chiura, Hiroshi Xavier; Kogure, Kazuhiro; Hamasaki, Koji

2015-10-01

A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8T, was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53T. The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name Fabibacter misakiensis sp. nov. The type strain is SK-8T ( = NBRC 110216T = KCTC 32969T).

Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj

2014-07-01

Two strains of Gram-negative, methylotrophic bacteria, isolated because of their abilities to promote plant growth, were subjected to a polyphasic taxonomic study. The isolates were strictly aerobic, motile, pink-pigmented, facultatively methylotrophic, non-spore-forming rods. The chemotaxonomic characteristics of the isolates included the presence of C18 : 1ω7c as the major cellular fatty acid. The DNA G+C contents of strains BL36(T) and BL47(T) were 69.4 and 69.8 mol%, respectively. 16S rRNA gene sequence analysis of strains BL36(T) and BL47(T) placed them under the genus Methylobacterium, with the pairwise sequence similarity between them and the type strains of closely related species ranging from 97.2 to 99.0%. On the basis of their phenotypic and phylogenetic distinctiveness and the results of DNA-DNA hybridization analysis, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium pseudosasicola sp. nov. (type strain BL36(T) = NBRC 105203(T) = ICMP 17621(T)) and Methylobacterium phyllostachyos sp. nov. (type strain BL47(T) = NBRC 105206(T) = ICMP 17619(T)) are proposed. © 2014 IUMS.

Oxidative damage of 18S and 5S ribosomal RNA in digestive gland of mussels exposed to trace metals.

PubMed

Kournoutou, Georgia G; Giannopoulou, Panagiota C; Sazakli, Eleni; Leotsinidis, Michel; Kalpaxis, Dimitrios L

2017-11-01

Numerous studies have shown the ability of trace metals to accumulate in marine organisms and cause oxidative stress that leads to perturbations in many important intracellular processes, including protein synthesis. This study is mainly focused on the exploration of structural changes, like base modifications, scissions, and conformational changes, caused in 18S and 5S ribosomal RNA (rRNA) isolated from the mussel Mytilus galloprovincialis exposed to 40μg/L Cu, 30μg/L Hg, or 100μg/L Cd, for 5 or 15days. 18S rRNA and 5S rRNA are components of the small and large ribosomal subunit, respectively, found in complex with ribosomal proteins, translation factors and other auxiliary components (metal ions, toxins etc). 18S rRNA plays crucial roles in all stages of protein synthesis, while 5S rRNA serves as a master signal transducer between several functional regions of 28S rRNA. Therefore, structural changes in these ribosomal constituents could affect the basic functions of ribosomes and hence the normal metabolism of cells. Especially, 18S rRNA along with ribosomal proteins forms the decoding centre that ensures the correct codon-anticodon pairing. As exemplified by ELISA, primer extension analysis and DMS footprinting analysis, each metal caused oxidative damage to rRNA, depending on the nature of metal ion and the duration of exposure. Interestingly, exposure of mussels to Cu or Hg caused structural alterations in 5S rRNA, localized in paired regions and within loops A, B, C, and E, leading to a continuous progressive loss of the 5S RNA structural integrity. In contrast, structural impairments of 5S rRNA in mussels exposed to Cd were accumulating for the initial 5days, and then progressively decreased to almost the normal level by day 15, probably due to the parallel elevation of metallothionein content that depletes the pools of free Cd. Regions of interest in 18S rRNA, such as the decoding centre, sites implicated in the binding of tRNAs (A- and P-sites) or translation factors, and areas related to translation fidelity, were found to undergo significant metal-induced conformational alterations, leading either to loosening of their structure or to more compact folding. These modifications were associated with parallel alterations in the translation process at multiple levels, a fact suggesting that structural perturbations in ribosomes, caused by metals, pose significant hurdles in translational efficiency and fidelity. Copyright © 2017 Elsevier B.V. All rights reserved.

Assembly constraints drive co-evolution among ribosomal constituents.

PubMed

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Prey-dependent retention of dimethylsulfoniopropionate (DMSP) by mixotrophic dinoflagellates.

PubMed

Lee, Hyunwoo; Park, Ki-Tae; Lee, Kitack; Jeong, Hae Jin; Yoo, Yeong Du

2012-03-01

We investigated the retention of dimethylsulfoniopropionate (DMSP) in phototrophic dinoflagellates arising from mixotrophy by estimating the cellular content of DMSP in Karlodinium veneficum (mixotrophic growth) fed for 7-10 days on either DMSP-rich Amphidinium carterae (phototrophic growth only) or DMSP-poor Teleaulax sp. (phototrophic growth only). In K. veneficum fed on DMSP-poor prey, the cellular content of DMSP remained almost unchanged regardless of the rate of feeding, whereas the cellular content of DMSP in cells of K. veneficum fed on DMSP-rich prey increased by as much as 21 times the cellular concentration derived exclusively from phototrophic growth. In both cases, significant fractions (10-32% in the former case and 55-65% in the latter) of the total DMSP ingested by K. veneficum were transformed into dimethylsulfide and other biochemical compounds. The results may indicate that the DMSP content of prey species affects temporal variations in the cellular DMSP content of mixotrophic dinoflagellates, and that mixotrophic dinoflagellates produce DMS through grazing on DMSP-rich preys. Additional studies should be performed to examine the universality of our finding in other mixotrophic dinoflagellates feeding on diverse prey species. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion | Center for Cancer Research

Cancer.gov

In Escherichia coli the genome must be compacted ∼1,000-fold to be contained in a cellular structure termed the nucleoid. It is proposed that the structure of the nucleoid is determined by a balance of multiple compaction forces and one major expansion force. The latter is mediated by transertion, a coupling of transcription, translation, and translocation of nascent membrane

[Identification of Hydrocarbon-Oxidizing Dietzia Bacteria from Petroleum Reservoirs Based on Phenotypic Properties and Analysis of the 16S rRNA and gyrB Genes].

PubMed

Nazina, T N; Shumkova, E S; Sokolova, D Sh; Babich, T L; Zhurina, M V; Xue, Yan-Fen; Osipov, G A; Poltaraus, A B; Tourova, T P

2015-01-01

The taxonomic position of hydrocarbon-oxidizing bacterial strains 263 and 32d isolated from formation water of the Daqing petroleum reservoir (PRC) was determined by polyphasic taxonomy techniques, including analysis of the 16S rRNA and the gyrB genes. The major chemotaxonomic characteristics of both strains, including the IV type cell wall, composition of cell wall fatty acids, mycolic acids, and menaquinones, agreed with those typical of Dietzia strains. The DNA G+C content of strains 263 and 32d were 67.8 and 67.6 mol%, respectively. Phylogenetic analysis of the 16S rRNA gene of strain 32d revealed 99.7% similarity to the gene of D. maris, making it possible to identify strain 32d as belonging to this species. The 16S rRNA gene sequence of strain 263 exhibited 99.7 and 99.9% similarity to those of D. natronolimnaea and D. cercidiphylli YIM65002(T), respectively. Analysis of the gyrB genes of the subterranean isolates and of a number of Dietzia type strains confirmed classiffication of strain 32d as a D. maris strain and of strain 263, as a D. natronolimnaea strain. A conclusion was made concerning higher resolving power of phylogenetic analysis of the gyrB gene compared to the 16S rRNA gene analysis in the case of determination of the species position of Dietzia isolates.

The complete mitochondrial genome sequence of Eimeria innocua (Eimeriidae, Coccidia, Apicomplexa).

PubMed

Hafeez, Mian Abdul; Vrba, Vladimir; Barta, John Robert

2016-07-01

The complete mitochondrial genome of Eimeria innocua KR strain (Eimeriidae, Coccidia, Apicomplexa) was sequenced. This coccidium infects turkeys (Meleagris gallopavo), Bobwhite quails (Colinus virginianus), and Grey partridges (Perdix perdix). Genome organization and gene contents were comparable with other Eimeria spp. infecting galliform birds. The circular-mapping mt genome of E. innocua is 6247 bp in length with three protein-coding genes (cox1, cox3, and cytb), 19 gene fragments encoding large subunit (LSU) rRNA and 14 gene fragments encoding small subunit (SSU) rRNA. Like other Apicomplexa, no tRNA was encoded. The mitochondrial genome of E. innocua confirms its close phylogenetic affinities to Eimeria dispersa.

Growth and cellular ion content of a salt-sensitive symbiotic system Azolla pinnata-Anabaena azollae under NaCl stress.

PubMed

Rai, Vandna; Sharma, Naveen Kumar; Rai, Ashwani K

2006-09-01

Salinity, at a concentration of 10 mM NaCl affected the growth of Azolla pinnata-Anabaena azollae association and became lethal at 40 mM. Plants exposed up to 30 mM NaCl exhibited longer roots than the control, especially during the beginning of incubation. Average root number in plants exposed to 10 and 20 mM NaCl remained almost the same as in control. A further rise in NaCl concentration to 30 mM reduced the root number, and roots shed off at 40 mM NaCl. Presence of NaCl in the nutrient solution increased the cellular Na+ of the intact association exhibiting differential accumulation by individual partners, while it reduced the cellular Ca2+ level. However, cellular K+ content did not show significant change. Cellular Na+ based on fresh weight of respective individual partners (host tissues and cyanobiont) remained higher in the host tissues than the cyanobiont, while reverse was true for K+ and Ca2+ contents. The contribution of A. azollae in the total cellular ion content of the association was a little because of meagre contribution of the cyanobiont mass (19-21%). High salt sensitivity of Azolla-Anabaena complex is due to an inability of the association to maintain low Na+ and high Ca2+ cellular level.

Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum.

PubMed

Oshkin, Igor Y; Belova, Svetlana E; Danilova, Olga V; Miroshnikov, Kirill K; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Liesack, Werner; Dedysh, Svetlana N

2016-06-01

Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, northern Russia. Cells of these three strains were Gram-stain-negative, light-pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme and utilized only methane and methanol. Strains Sph1T, Sph2 and OZ2 were able to grow at a pH range of 4.0-8.9 (optimum at pH 6.0-7.0) and at temperatures between 2 and 36 °C. Although their temperature optimum was at 20-25 °C, these methanotrophs grew well at lower temperatures, down to 4 °C. The major cellular fatty acids were C16 : 1ω5c, C16 : 1ω6c, C16 : 1ω7c, C16 : 1ω8c, C16 : 0 and C14 : 0; the DNA G+C content was 51.4-51.9 mol%. Strains Sph1T, Sph2 and OZ2 displayed nearly identical (99.1-99.7 % similarity) 16S rRNA gene sequences and belonged to the family Methylococcaceae of the class Gammaproteobacteria. The most closely related organism was Methylovulum miyakonense HT12T (96.0-96.5 % 16S rRNA gene sequence similarity and 90 % pmoA sequence similarity). The novel isolates, however, differed from Methylovulum miyakonense HT12T by cell morphology, pigmentation, absence of soluble methane monooxygenase, more active growth at low temperatures, growth over a broader pH range and higher DNA G+C content. On the basis of these differences, we propose a novel species, Methylovulum psychrotolerans sp. nov., to accommodate these methanotrophs. Strain Sph1T (=LMG 29227T=VKM B-3018T) is the type strain.

A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization.

PubMed

Behr, T; Koob, C; Schedl, M; Mehlen, A; Meier, H; Knopp, D; Frahm, E; Obst, U; Schleifer, K; Niessner, R; Ludwig, W

2000-12-01

Complete 23S and almost complete 16S rRNA gene sequences were determined for the type strains of the validly described Enterococcus species, Melissococcus pluton and Tetragenococcus halophilus. A comprehensive set of rRNA targeted specific oligonucleotide hybridization probes was designed according to the multiple probe concept. In silico probe design and evaluation was performed using the respective tools of the ARB program package in combination with the ARB databases comprising the currently available 16S as well as 23S rRNA primary structures. The probes were optimized with respect to their application for reverse hybridization in microplate format. The target comprising 16S and 23S rDNA was amplified and labeled by PCR (polymerase chain reaction) using general primers targeting a wide spectrum of bacteria. Alternatively, amplification of two adjacent rDNA fragments of enterococci was performed by using specific primers. In vitro evaluation of the probe set was done including all Enterococcus type strains, and a selection of other representatives of the gram-positive bacteria with a low genomic DNA G+C content. The optimized probe set was used to analyze enriched drinking water samples as well as original samples from waste water treatment plants.

Bacillus Strains Most Closely Related to Bacillus nealsonii Are Not Effectively Circumscribed within the Taxonomic Species Definition

PubMed Central

Peak, K. Kealy; Duncan, Kathleen E.; Luna, Vicki A.; King, Debra S.; McCarthy, Peter J.; Cannons, Andrew C.

2011-01-01

Bacillus strains with >99.7% 16S rRNA gene sequence similarity were characterized with DNA:DNA hybridization, cellular fatty acid (CFA) analysis, and testing of 100 phenotypic traits. When paired with the most closely related type strain, percent DNA:DNA similarities (% S) for six Bacillus strains were all far below the recommended 70% threshold value for species circumscription with Bacillus nealsonii. An apparent genomic group of four Bacillus strain pairings with 94%–70% S was contradicted by the failure of the strains to cluster in CFA- and phenotype-based dendrograms as well as by their differentiation with 9–13 species level discriminators such as nitrate reduction, temperature range, and acid production from carbohydrates. The novel Bacillus strains were monophyletic and very closely related based on 16S rRNA gene sequence. Coherent genomic groups were not however supported by similarly organized phenotypic clusters. Therefore, the strains were not effectively circumscribed within the taxonomic species definition. PMID:22046187

Microbial detection with low molecular weight RNA.

PubMed

Kourentzi, K D; Fox, G E; Willson, R C

2001-12-01

The need to monitor microorganisms in the environment has increased interest in assays based on hybridization probes that target nucleic acids (e.g., rRNA). We report the development of liquid-phase assays for specific bacterial 5S rRNA sequences or similarly sized artificial RNAs (aRNAs) using molecular beacon technology. These beacons fluoresce only in the presence of specific target sequences, rendering as much as a 27-fold fluorescence enhancement. The assays can be used with both crude cell lysates and purified total RNA preparations. Minimal sample preparation (e.g., heating to promote leakage from cells) is sufficient to detect many Gram-negative bacteria. Using this approach it was possible to detect an aRNA-labeled Escherichia coli strain in the presence of a large background of an otherwise identical E. coli strain. Finally, by using a longer wavelength carboxytetramethylrhodamine beacon it was possible to reduce the fraction of the signal due to cellular autofluorescence to below 0.5%.

Microbial detection with low molecular weight RNA

NASA Technical Reports Server (NTRS)

Kourentzi, K. D.; Fox, G. E.; Willson, R. C.

2001-01-01

The need to monitor microorganisms in the environment has increased interest in assays based on hybridization probes that target nucleic acids (e.g., rRNA). We report the development of liquid-phase assays for specific bacterial 5S rRNA sequences or similarly sized artificial RNAs (aRNAs) using molecular beacon technology. These beacons fluoresce only in the presence of specific target sequences, rendering as much as a 27-fold fluorescence enhancement. The assays can be used with both crude cell lysates and purified total RNA preparations. Minimal sample preparation (e.g., heating to promote leakage from cells) is sufficient to detect many Gram-negative bacteria. Using this approach it was possible to detect an aRNA-labeled Escherichia coli strain in the presence of a large background of an otherwise identical E. coli strain. Finally, by using a longer wavelength carboxytetramethylrhodamine beacon it was possible to reduce the fraction of the signal due to cellular autofluorescence to below 0.5%.

Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds

PubMed Central

Morita, Hidetoshi; Shiratori, Chiharu; Murakami, Masaru; Takami, Hideto; Kato, Yukio; Endo, Akihito; Nakajima, Fumihiko; Takagi, Misako; Akita, Hiroaki; Okada, Sanae; Masaoka, Toshio

2007-01-01

Two strains, KBL13T and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13T and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA–DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13T and GBL13, belong to the same species. In the representative strain, KBL13T, the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231T (=ATCC 11741T; AF089108) is the type strain most closely related to the strain KBL13T as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA–DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13T represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13T (=JCM 14209T=DSM 18933T). PMID:18048734

Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds.

PubMed

Morita, Hidetoshi; Shiratori, Chiharu; Murakami, Masaru; Takami, Hideto; Kato, Yukio; Endo, Akihito; Nakajima, Fumihiko; Takagi, Misako; Akita, Hiroaki; Okada, Sanae; Masaoka, Toshio

2007-12-01

Two strains, KBL13(T) and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13(T) and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA-DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13(T) and GBL13, belong to the same species. In the representative strain, KBL13(T), the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231(T) (=ATCC 11741(T); AF089108) is the type strain most closely related to the strain KBL13(T) as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA-DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13(T) represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13(T) (=JCM 14209(T)=DSM 18933(T)).

RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

PubMed

Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

2007-02-08

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

Equally parsimonious pathways through an RNA sequence space are not equally likely

NASA Technical Reports Server (NTRS)

Lee, Y. H.; DSouza, L. M.; Fox, G. E.

1997-01-01

An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.

Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost.

PubMed

Moriya, Toshiyuki; Hikota, Tomohisa; Yumoto, Isao; Ito, Takashi; Terui, Yusuke; Yamagishi, Akihiko; Oshima, Tairo

2011-03-01

Two novel thermophilic micro-organisms, designated YMO81(T) and YMO722(T), were isolated from a high-temperature compost (internal temperature > 95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3 x 4.0 μm). Spore formation was not observed. Strain YMO81(T) grew at 83 °C and pH 6.9-8.9 and grew optimally at 78 °C and pH 7.5 with 2  % NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81(T) also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C₁₇:₀ and anteiso-C₁₇:₀. The DNA G+C contents of strains YMO81(T) and YMO722(T) were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5(T) (90 % 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain YMO722(T) and strain YMO81(T) was 55  %. N⁴-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81(T) (=ATCC BAA-1462(T) =JCM 14719(T) =DSM 45223(T)), and Calditerricola yamamurae sp. nov., with type strain YMO722(T) (=ATCC BAA-1461(T) =JCM 14720(T) =DSM 45224(T)).

Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants.

PubMed

Kim, Tae-Su; Han, Ji-Hye; Joung, Yochan; Kim, Seung Bum

2015-08-01

Two Gram-staining-positive, aerobic, endospore-forming, motile bacteria, strains DT7-4T and DLE-12T, were isolated from roots of evening primrose (Oenothera biennis) and day lily (Hemerocallis fulva), respectively, and subjected to taxonomic characterization. Analysis of 16S rRNA gene sequences indicated that the two strains fell into two distinct phylogenetic clusters belonging to the genus Paenibacillus. Strain DT7-4T was most closely related to Paenibacillus phyllosphaerae PALXIL04T and Paenibacillus taihuensis THMBG22T, with 96.3% 16S rRNA gene sequence similarity to each, and strain DLE-12T was most closely related to Paenibacillus ginsengarvi Gsoil 139T and Paenibacillus hodogayensis SGT, with 96.6 and 93.3% sequence similarity, respectively. Both isolates contained anteiso-C15 : 0 as the dominant fatty acid, meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and MK-7 as the respiratory menaquinone. The cellular polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified polar lipids. The DNA G+C contents of strains DT7-4T and DLE-12T were 50.1 ± 0.7 and 55.2 ± 0.5 mol%, respectively. The chemotaxonomic properties of both isolates were typical of members of the genus Paenibacillus. However, our biochemical and phylogenetic analyses distinguished each isolate from related species. Based on our polyphasic taxonomic analysis, strains DT7-4T and DLE-12T should be recognized as representatives of novel species of Paenibacillus, for which the names Paenibacillus oenotherae sp. nov. (type strain DT7-4T = KCTC 33186T = JCM 19573T) and Paenibacillus hemerocallicola sp. nov. (type strain DLE-12T = KCTC 33185T = JCM 19572T) are proposed.

Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales.

PubMed

Cavaletti, Linda; Monciardini, Paolo; Schumann, Peter; Rohde, Manfred; Bamonte, Ruggiero; Busti, Elena; Sosio, Margherita; Donadio, Stefano

2006-08-01

Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C(15 : 0), i-C(16 : 0) and ai-C(15 : 0) and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766(T) and galactose in strain GE134769(T)). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769(T) (=DSM 44927(T)=NRRL B-24432(T)) and GE134766(T) (=DSM 44926(T)=NRRL B-24431(T)), respectively. The DNA G+C contents of strains GE134769(T) and GE134766(T) are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome

PubMed Central

Schmidt, Johanna; Taipale, Sami J.; Doolittle, W. Ford; Koll, Ulrike

2014-01-01

A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T ( = DSM 23834T = LMG 26932T). PMID:24984700

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

PubMed

Hahn, Martin W; Schmidt, Johanna; Taipale, Sami J; Doolittle, W Ford; Koll, Ulrike

2014-09-01

A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)). © 2014 IUMS.

Kiloniella antarctica sp. nov., isolated from a polynya of Amundsen Sea in Western Antarctic Sea.

PubMed

Si, Ok-Ja; Yang, Hye-Young; Hwang, Chung Yeon; Kim, So-Jeong; Choi, Sun-Bin; Kim, Jong-Geol; Jung, Man-Young; Kim, Song-Gun; Roh, Seong Woon; Rhee, Sung-Keun

2017-07-01

A taxonomic study was conducted on strain soj2014T, which was isolated from the surface water of a polynya in the Antarctic Sea. Comparative 16S rRNA gene sequence analysis showed that strain soj2014T belongs to the family Kiloniellaceae and is closely related to Kiloniella spongiae MEBiC09566T, 'Kiloniella litopenaei' P1-1T and Kiloniella laminariae LD81T (98.0 %, 97.8 % and 96.2 % 16S rRNA gene sequence similarity, respectively). The DNA-DNA hybridization values between strain soj2014T and closely related strains were below 28.6 %. The G+C content of the genomic DNA of strain soj2014T was 45.5 mol%. The predominant cellular fatty acids were summed feature 8 (composed of C18 : 1ω6c/C18 : 1ω7c, 57.0 %) and summed feature 3 (composed of C16 : 1ω6c/C16 : 1ω7c, 23.5 %). Strain soj2014T was Gram-stain-negative, slightly curved, spiral-shaped, and motile with a single polar flagellum. The strain grew at 0-30 °C (optimum, 25 °C), in 1.5-5.1 % (w/v) NaCl (optimum, 2.1-2.4 %) and at pH 5.5-9.5 (optimum, 7.5-8.0). It also had differential carbohydrate utilization traits and enzyme activities compared with closely related strains. Based on these phylogenetic, phenotypic and chemotaxonomic analyses, strain soj2014T represents a distinct species, separable from the reference strains, and is, therefore, proposed as a novel species, Kiloniella antarctica sp. nov. The type strain is soj2014T (=KCTC 42186T=JCM 30386T).

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.

PubMed

Xie, Cheng-Hui; Yokota, Akira

2005-11-01

The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599T, IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368T. It was found that the type strain of Alcaligenes latus, IAM 12599T, showed 99 x 9 and 96 x 1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA-DNA hybridization suggested that strains IAM 12599T and IAM 12665 belong to a single species (89 x 7 %) and that strain IAM 12664 (35 x 1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599T=DSM 1122T=LMG 3321T=ATCC 29712T; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664T=DSM 1124T=LMG 3324T=ATCC 29713T). Pseudomonas saccharophila IAM 14368T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96 x 8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368T (=LMG 2256T=ATCC 15946T).

Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen

NASA Astrophysics Data System (ADS)

Sundset, Monica A.; Kohn, Alexandra; Mathiesen, Svein D.; Præsteng, Kirsti E.

2008-08-01

Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer ( Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 × 2.0-3.5 μm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

Paenibacillus lentus sp. nov., a β-mannanolytic bacterium isolated from mixed soil samples in a selective enrichment using guar gum as the sole carbon source.

PubMed

Li, Yong-Fu; Calley, John N; Ebert, Philip J; Helmes, Emily Bulian

2014-04-01

A novel bacterial strain, CMG1240(T), was isolated in 1988 from mixed soil samples collected from the United States and South America in a selective enrichment medium with guar gum as the sole carbon source. This microbial isolate showed β-mannanolytic activity to hydrolyse the galactomannans present in guar gum. Strain CMG1240(T) was aerobic, Gram-stain-variable, non-motile, rod-shaped and endospore-forming. It was further examined based on a combination of phenotypic, physiological and genetic characterization. On the basis of 16S rRNA gene sequence similarity, cellular lipid profile and fatty acid composition, strain CMG1240(T) was shown to belong unequivocally to the genus Paenibacillus. Quinone analysis showed that MK-7 was the only menaquinone detected. The main cell-wall sugar was xylose with trace amounts of mannose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unknown glycolipids, phospholipids, phosphoglycolipids and other lipids. The peptidoglycan structure was A1γ (meso-diaminopimelic acid-direct). The major fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content was 46 mol% as determined experimentally and by analysis of the genomic sequence. The 16S rRNA gene sequence of strain CMG1240(T) shared highest similarity with that of Paenibacillus fonticola ZL(T) (97.6 %) while all other tested Paenibacillus strains showed lower sequence similarities (≤95.3 %). The results of DNA-DNA hybridization and chemotaxonomic tests enabled the genotypic and phenotypic differentiation of strain CMG1240(T) from P. fonticola. Based on these results, strain CMG1240(T) ( = ATCC BAA-2594(T) = DSM 25539(T)) should be designated the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus lentus sp. nov. is proposed.

Halomonas garicola sp. nov., isolated from saeu-jeot, a Korean salted and fermented shrimp sauce.

PubMed

Jung, Woo Yong; Lee, Hyo Jung; Jeon, Che Ok

2016-02-01

A Gram-stain-negative, moderately halophilic and facultatively aerobic bacterium capable of respiration with nitrate, designated strain JJ-M1 T , was isolated from saeu-jeot, a traditional Korean fermented shrimp sauce. Cells of the strain were non-motile short rods showing oxidase-negative and catalase-positive reactions and the production of pale-yellow pigments. Growth of strain JJ-M1 T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 3-22.5 % (w/v) sea salts (optimum, 10 %). Strain JJ-M1 T contained ubiquinone 9 (Q-9) as the predominant isoprenoid quinone and summed feature 8 (comprising C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ), C 16 : 0 , summed feature 3 (comprising C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) and C 12 : 0 3-OH as the major cellular fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content of strain JJ-M1 T was 62.4 mol%. Phylogenetic and comparative analyses, based on 16S rRNA gene sequences, indicated that strain JJ-M1 T formed a tight phyletic lineage with Halomonas jeotgali Hwa T within the genus Halomonas and was most closely related to Halomonas jeotgali Hwa T with 96.2 % 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic features, strain JJ-M1 T represents a novel species of the genus Halomonas , for which the name Halomonas garicola sp. nov. is proposed. The type strain is JJ-M1 T ( = KACC 18117 T  = JCM 30151 T ).

Multicolor microRNA FISH effectively differentiates tumor types

PubMed Central

Renwick, Neil; Cekan, Pavol; Masry, Paul A.; McGeary, Sean E.; Miller, Jason B.; Hafner, Markus; Li, Zhen; Mihailovic, Aleksandra; Morozov, Pavel; Brown, Miguel; Gogakos, Tasos; Mobin, Mehrpouya B.; Snorrason, Einar L.; Feilotter, Harriet E.; Zhang, Xiao; Perlis, Clifford S.; Wu, Hong; Suárez-Fariñas, Mayte; Feng, Huichen; Shuda, Masahiro; Moore, Patrick S.; Tron, Victor A.; Chang, Yuan; Tuschl, Thomas

2013-01-01

MicroRNAs (miRNAs) are excellent tumor biomarkers because of their cell-type specificity and abundance. However, many miRNA detection methods, such as real-time PCR, obliterate valuable visuospatial information in tissue samples. To enable miRNA visualization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA FISH. As a proof of concept, we used this method to differentiate two skin tumors, basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), with overlapping histologic features but distinct cellular origins. Using sequencing-based miRNA profiling and discriminant analysis, we identified the tumor-specific miRNAs miR-205 and miR-375 in BCC and MCC, respectively. We addressed three major shortcomings in miRNA FISH, identifying optimal conditions for miRNA fixation and ribosomal RNA (rRNA) retention using model compounds and high-pressure liquid chromatography (HPLC) analyses, enhancing signal amplification and detection by increasing probe-hapten linker lengths, and improving probe specificity using shortened probes with minimal rRNA sequence complementarity. We validated our method on 4 BCC and 12 MCC tumors. Amplified miR-205 and miR-375 signals were normalized against directly detectable reference rRNA signals. Tumors were classified using predefined cutoff values, and all were correctly identified in blinded analysis. Our study establishes a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues. PMID:23728175

Comparison of plastid 16S rRNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta).

PubMed

Tartar, Aurélien; Boucias, Drion G; Becnel, James J; Adams, Byron J

2003-11-01

The Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60.7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes.

Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits.

PubMed

Vela, Ana I; Casas-Díaz, Encarna; Lavín, Santiago; Domínguez, Lucas; Fernández-Garayzábal, Jose F

2015-09-01

Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03(T) (96.9% 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03(T) (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9%, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796B(T) ( = CECT 8754(T) = CCUG 66496(T)).

[Methylophaga murata sp. nov.: a haloalkaliphilic aerobic methylotroph from deteriorating marble].

PubMed

Doronina, N V; Li, Ts D; Ivanova, E G; Trotsenko, Iu A

2005-01-01

The haloalkaliphilic methylotrophic bacterium (strain Kr3) isolated from material scraped off the deteriorating marble of the Moscow Kremlin masonry has been found to be able to utilize methanol, methylamine, trimethylamine, and fructose as carbon and energy sources. Its cells are gram-negative motile rods multiplying by binary fission. Spores are not produced. The isolate is strictly aerobic and requires vitamin B12 and Na+ ions for growth. It is oxidase- and catalase-positive and reduces nitrates to nitrites. Growth occurs at temperatures between 0 and 42 degrees C (with the optimum temperatures being 20-32 degrees C), pH values between 6 and 11 (with the optimum at 8-9), and NaCl concentrations between 0.05 and 3 M (with the optimum at 0.5-1.5 M). The dominant cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. The major cellular fatty acids are palmitic (C16:0), palmitoleic (C16:1), and octadecenoic (C18:1) acids. The major ubiquinone is Q8. The isolate accumulates ectoine and glutamate, as well as a certain amount of sucrose, to function as osmoprotectants and synthesizes an exopolysaccharide composed of carbohydrate and protein components. It is resistant to heating at 70 degrees C, freezing, and drying; utilizes methanol, with the resulting production of formic acid, which is responsible for the marble-degrading activity of the isolate; and implements the 2-keto-3-deoxy-6-phosphogluconate variant of the ribulose monophosphate pathway. The G+C content of its DNA is 44.6 mol%. Based on 16S rRNA gene sequencing and DNA-DNA homology levels (23-41%) with neutrophilic and alkaliphilic methylobacteria from the genus Methylophaga, the isolate has been identified as a new species, Methylophaga murata (VKM B-2303T = NCIMB 13993T).

The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales.

PubMed

Sakai, Masao; Hosoda, Akifumi; Ogura, Kenjiro; Ikenaga, Makoto

2014-01-01

An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5-B(T), belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FS(T), at the species level with 96.5% similarity. Strain KA5-B(T) was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15-37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0-8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso-C15:0, C16:1ω7c, and iso-C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FS(T) was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5-B(T) (JCM 18477(T) = KCTC 32107(T)) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed.

Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius type strain D43(T) isolated from fermented seafood.

PubMed

Lee, Hae-Won; Kim, Dae-Won; Lee, Mi-Hwa; Kim, Byung-Yong; Cho, Yong-Joon; Yim, Kyung June; Song, Hye Seon; Rhee, Jin-Kyu; Seo, Myung-Ji; Choi, Hak-Jong; Choi, Jong-Soon; Lee, Dong-Gi; Yoon, Changmann; Nam, Young-Do; Roh, Seong Woon

2015-01-01

An extremely halophilic archaeon, Haladaptatus cibarius D43(T), was isolated from traditional Korean salt-rich fermented seafood. Strain D43(T) shows the highest 16S rRNA gene sequence similarity (98.7 %) with Haladaptatus litoreus RO1-28(T), is Gram-negative staining, motile, and extremely halophilic. Despite potential industrial applications of extremely halophilic archaea, their genome characteristics remain obscure. Here, we describe the whole genome sequence and annotated features of strain D43(T). The 3,926,724 bp genome includes 4,092 protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C content of 57.76 %.

Toxicological Tipping Points: Learning Boolean Networks from High-Content Imaging Data. (BOSC meeting)

EPA Science Inventory

The objective of this work is to elucidate biological networks underlying cellular tipping points using time-course data. We discretized the high-content imaging (HCI) data and inferred Boolean networks (BNs) that could accurately predict dynamic cellular trajectories. We found t...

The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).

PubMed

Tian, Si-Qin; Cui, Ping; Fang, Su-Fang; Liu, Guo-Hua; Wang, Chun-Ren; Zhu, Xing-Quan

2015-01-01

In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis.

Pseudopropionibacterium sp. nov., a novel red-pigmented species isolated from human gingival sulcus.

PubMed

Saito, Masanori; Shinozaki-Kuwahara, Noriko; Tsudukibashi, Osamu; Hashizume-Takizawa, Tomomi; Kobayashi, Ryoki; Kurita-Ochiai, Tomoko

2018-04-24

Strain SK-1 T is a novel Gram stain-positive, pleomorphic, rod-shaped, non-spore forming, and non-motile organism, designated SK-1 T , isolated from human gingival sulcus that produces acetic acid, propionic acid, lactic acid, and succinic acid as end products of glucose fermentation. Strain SK-1 T had the closest relatedness to Pseudopropionibacterium (Propionibacterium) propionicum with sequence homologies of the 16S rRNA and RNA polymerase β subunit (rpoB) genes of 96.6% and 93.1%, respectively. The genomic DNA G + C content of the isolate was 61.8 mol%. Based on the sequence data of the 16S rRNA and housekeeping (rpoB) genes, we propose a novel taxon, Pseudopropionibacterium rubrum sp. nov. (type strain SK-1 T = JCM 31317T= DSM 100122T). The 16S rRNA and rpoB gene sequences of strain SK-1 T were deposited to the DNA Data Bank of Japan under the accession numbers LC002971 and LC102236, respectively. © 2018 The Societies and John Wiley & Sons Australia, Ltd.

Characterization and Screening of Native Scenedesmus sp. Isolates Suitable for Biofuel Feedstock.

PubMed

Gour, Rakesh Singh; Chawla, Aseem; Singh, Harvinder; Chauhan, Rajinder Singh; Kant, Anil

2016-01-01

In current study isolates of two native microalgae species were screened on the basis of growth kinetics and lipid accumulation potential. On the basis of data obtained on growth parameters and lipid accumulation, it is concluded that Scenedesmus dimorphus has better potential as biofuel feedstock. Two of the isolates of Scenedesmus dimorphus performed better than other isolates with respect to important growth parameters with lipid content of ~30% of dry biomass. Scenedesmus dimorphus was found to be more suitable as biodiesel feedstock candidate on the basis of cumulative occurrence of five important biodiesel fatty acids, relative occurrence of SFA (53.04%), MUFA (23.81%) and PUFA (19.69%), and more importantly that of oleic acid in its total lipids. The morphological observations using light and Scanning Electron Microscope and molecular characterization using amplified 18S rRNA gene sequences of microalgae species under study were also performed. Amplified 18S rRNA gene fragments of the microalgae species were sequenced, annotated at the NCBI website and phylogenetic analysis was done. We have published eight 18S rRNA gene sequences of microalgae species in NCBI GenBank.

Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs.

PubMed

Mann, Evelyne; Wetzels, Stefanie U; Pinior, Beate; Metzler-Zebeli, Barbara U; Wagner, Martin; Schmitz-Esser, Stephan

2016-07-01

The aim of this study was to disentangle the microbial diversity on porcine musculature. The hypervariable V1-V2 region of the 16S rRNA gene was amplified from DNA samples of clinically healthy slaughter pigs (n=8). Pyrosequencing yielded 37,000 quality-controlled reads and a diverse microbiome with 54-159 OTUs per sample was detected. Interestingly, 6 out of 8 samples were strongly dominated by 1-2 highly abundant OTUs (best hits of highly abundant OTUs: Serratia proteamaculans, Pseudomonas syringae, Aeromonas allosaccharophila, Brochothrix thermosphacta, Acidiphilium cryptum and Escherichia coli). In 1g musculature scraping, 3.20E+06 16S rRNA gene copies and 4.45E+01 Enterobacteriaceae rRNA gene copies were detected with qPCR. We conclude that i.) next-generation sequencing technologies help encompass the full content of complex, bacterial contamination, ii.) psychrophile spoilers dominated the microbiota and iii.) E. coli is an effective marker species for pork contamination, as it was one of very few abundant species being present in all samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments.

PubMed

Hakil, Florence; Amin-Ali, Oulfat; Hirschler-Réa, Agnès; Mollex, Damien; Grossi, Vincent; Duran, Robert; Matheron, Robert; Cravo-Laureau, Cristiana

2014-02-01

A novel sulfate-reducing bacterium designated strain BE2801(T) was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801(T) occurred at 30-32 °C, 0.5-1.5% NaCl (w/v) and pH 7.2-7.4. Strain BE2801(T) grew with C4 to C20 fatty acids or C12 to C20 n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C(16 : 1)ω7c and C(18 : 1)ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801(T) was a member of the family Desulfobacteraceae within the class Deltaproteobacteria. DNA-DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801(T) ( = DSM 25524(T) = JCM 18157(T)) is proposed to be a representative of a novel species of the genus Desulfatiferula, for which the name Desulfatiferula berrensis sp. nov. is suggested.

Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai.

PubMed

Hyun, Dong-Wook; Shin, Na-Ri; Kim, Min-Soo; Kim, Pil Soo; Kim, Joon Yong; Whon, Tae Woong; Bae, Jin-Woo

2014-02-01

A novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80(T), was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7-8 and with 1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80(T) fell within the cluster of the genus Actinomyces, with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8% similarity) and Actinomyces urogenitalis (97.0% similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA-DNA hybridization values with closely related strains indicated less than 7.6% genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80(T) represents a novel species of the genus Actinomyces, for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80(T) ( = KACC 17211(T) = JCM 18848(T)).

Kocuria koreensis sp. nov., isolated from fermented seafood.

PubMed

Park, Eun-Jin; Roh, Seong Woon; Kim, Min-Soo; Jung, Mi-Ja; Shin, Kee-Sun; Bae, Jin-Woo

2010-01-01

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31(T), was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0-15.0 % (w/v) NaCl, and at pH 5-10 and 15-37 degrees C. Major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). Strain P31(T) contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31(T) was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31(T) was most closely related to Kocuria kristinae DSM 20032(T), with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA-DNA hybridization value between strain P31(T) and K. kristinae DSM 20032(T) was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31(T) represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31(T) (=KCTC 19595(T)=JCM 15915(T)).

Alicyclobacillus fodiniaquatilis sp. nov., isolated from acid mine water.

PubMed

Zhang, Bo; Wu, Yu-Fan; Song, Jin-Long; Huang, Zhong-Sheng; Wang, Bao-Jun; Liu, Shuang-Jiang; Jiang, Cheng-Ying

2015-12-01

Two novel, Gram-stain-variable, moderately thermophilic, acidophilic, rod-shaped, endospore-forming bacteria, G45-16T and G45-17, were isolated from acid mine water of Zijin copper mine in Fujian Province, China. Phylogenetic analysis of 16S rRNA gene sequences showed that they were closely related to Alicyclobacillus acidoterrestris ATCC 49025T with sequence similarities of 96.8 %. Cells grew aerobically at 20-45 °C (optimum, 40 °C), at pH 2.5-5.5(optimum, pH 3.5) and in the presence of 0-4.0 % (w/v) NaCl. Strains contained MK-7 as the major menaquinone and the major cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 51.3 and 49.8 mol% (Tm) for G45-16T and G45-17, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their relatives and DNA-DNA relatedness values, it is concluded that strains G45-16T and G45-17 represent a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus fodiniaquatilis sp. nov. is proposed; the type strain is G45-16T(=CGMCC 1.15049T=NBRC 111483T).

Paenibacillus guangzhouensis sp. nov., an Fe(III)- and humus-reducing bacterium from a forest soil.

PubMed

Li, Jibing; Lu, Qin; Liu, Ting; Zhou, Shungui; Yang, Guiqin; Zhao, Yong

2014-11-01

A Gram-reaction-variable, rod-shaped, motile, facultatively aerobic and endospore-forming bacterium, designated strain GSS02(T), was isolated from a forest soil. Strain GSS02(T) was capable of reducing humic substances and Fe(III) oxides. Strain GSS02(T) grew optimally at 35 °C, at pH 78 and in the presence of 1% NaCl. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C(15:0) and iso-C(16:0) and the polar lipid profile contained mainly phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol, with moderate amounts of two unknown aminophospholipids and a minor amount of one unknown lipid. The DNA G+C content was 53.4 mol%. Comparative 16S rRNA gene sequence analysis showed that strain GSS02(T) was related most closely to Paenibacillus terrigena JCM 21741(T) (98.1% similarity). Mean DNA-DNA relatedness between strain GSS02(T) and P. terrigena JCM 21741(T) was 58.8 ± 0.5%. The phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain GSS02(T) belongs to the genus Paenibacillus and represents a novel species, for which the name Paenibacillus guangzhouensis sp. nov. is proposed. The type strain is GSS02(T) ( =KCTC 33171(T) =CCTCC AB 2013236(T)). © 2014 IUMS.

Streptohalobacillus salinus gen. nov., sp. nov., a moderately halophilic, Gram-positive, facultative anaerobe isolated from subsurface saline soil.

PubMed

Wang, Xiaowei; Xue, Yanfen; Ma, Yanhe

2011-05-01

A Gram-stain-positive, rod-shaped, non-sporulating, motile and moderately halophilic bacterium, designated strain H96B60(T), was isolated from a saline soil sample of the Qaidam basin, China. The strain was facultatively anaerobic. Major end products formed from glucose fermentation were acetate, ethanol and lactic acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone component was menaquinone-6 (MK-6). The predominant cellular fatty acids were C(16: 0), anteiso-C(13 : 0) and anteiso-C(15 : 0). The genomic DNA G+C content of strain H96B60(T) was 36.2 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequences indicated that strain H96B60(T) represented a novel phyletic lineage within the family Bacillaceae and was related most closely to Halolactibacillus species (96.1-96.4 % similarity). Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain H96B60(T) is considered to represent a novel species of a new genus, for which the name Streptohalobacillus salinus gen. nov., sp. nov. is proposed. The type strain of Streptohalobacillus salinus is H96B60(T) ( = DSM 22440(T)  = CGMCC 1.7733(T)).

Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan.

PubMed

An, Sun-Young; Asahara, Mika; Goto, Keiichi; Kasai, Hiroaki; Yokota, Akira

2007-07-01

Two Gram-positive, round-spore-forming, rod-shaped, halophilic bacterial strains, 5B73C(T) and 5B133E, were isolated from field soil in Kakegawa, Shizuoka, Japan, and were characterized taxonomically using a polyphasic approach. These two strains were found to comprise strictly aerobic, motile rods that formed subterminal endospores. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains 5B73C(T) and 5B133E are phylogenetically affiliated to the genus Virgibacillus, exhibiting sequence similarities of 94.1-96.4 % with respect to the type strains of Virgibacillus species. The DNA G+C contents of strains 5B73C(T) and 5B133E were 42.6 and 42.3 mol%, respectively. The cell-wall peptidoglycan type (meso-diaminopimelic acid), the major cellular fatty acids (anteiso-C(15 : 0), iso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0)) and the quinone type (MK-7) of the isolates support their affiliation to the genus Virgibacillus. On the basis of their genotypic and phenotypic characteristics, the isolates represent a novel species of the genus Virgibacillus, for which the name Virgibacillus halophilus sp. nov. is proposed. The type strain is 5B73C(T) (=IAM 15308(T)=KCTC 13935(T)).

Paenibacillus methanolicus sp. nov., a xylanolytic, methanol-utilizing bacterium isolated from the phyllosphere of bamboo (Pseudosasa japonica).

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Saravanan, Venkatakrishnan Sivaraj; Pragatheswari, Dhandapani; Duraipandiyan, Veeramuthu; Al-Dhabi, Naif Abdullah; Santhanakrishnan, Palani

2016-11-01

Strain BL24T, isolated from bamboo phyllosphere collected in Coimbatore, India, was studied for taxonomic classification. Cells of the strain were aerobic, Gram-stain-positive, motile, catalase- and oxidase-positive rods and grew on media containing methanol. In 16S rRNA gene sequence analysis, strain BL24Tshowed the highest sequence similarities with Paenibacillus phyllosphaeraeKACC 11473T (97.8 %) and Paenibacillus sacheonensisSY01 (95.1 %). DNA-DNA hybridization with P. phyllosphaerae KACC 11473T, phylogenetically the most closely related species, was 21.6 %; this value showed that strain BL24Tbelonged to a different species. The cell-wall peptidoglycan was found to possess meso-diaminopimelic acid and the G+C content of genomic DNA was 52.1 mol %. It contained menaquinone (MK)-7 as the predominant respiratory quinone and the major cellular fatty acids are C16 : 0, anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0. Based on the molecular and chemotaxonomic markers and physiological properties, strain BL24T (=NRRL B-51698T=CCM 7577T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillusmethanolicusis proposed.

Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production.

PubMed

Paharkova, Vladislava; Alvarez, Griselda; Nakamura, Hiromi; Cohen, Pinchas; Lee, Kuk-Wha

2015-09-15

Evidence for the putative mitochondrial origin of the Humanin (HN) peptide has been lacking, although its cytoprotective activity has been demonstrated in a variety of organismal and cellular systems. We sought to establish proof-of-principle for a mitochondria-derived peptide (MDP) in a rat-derived cellular system as the rat HN sequence is predicted to lack nuclear insertions of mitochondrial origin (NUMT). We found that the rat HN (Rattin; rHN) homologue is derived from the mitochondrial genome as evidenced by decreased production in Rho-0 cells, and that peptide translation occurs in the mitochondria as it is unaffected by cycloheximide. Rat HN localizes to the mitochondria in cellular subfractionation and immunohistochemical studies. Addition of a HN analogue to isolated mitochondria from rat INS-1 beta cells reduced hydrogen peroxide production by 55%. In summary, a locally bioactive peptide is derived and translated from an open reading frame (ORF) within rat mitochondrial DNA encoding 16S rRNA. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

PubMed

Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

2015-04-01

Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

PubMed

Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

2016-01-01

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

PubMed Central

Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

2016-01-01

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota. PMID:26140533

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance ourmore » knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.« less

Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.

PubMed

Running, William E; Reilly, James P

2010-10-01

Ribosomes occupy a central position in cellular metabolism, converting stored genetic information into active cellular machinery. Ribosomal proteins modulate both the intrinsic function of the ribosome and its interaction with other cellular complexes, such as chaperonins or the signal recognition particle. Chemical modification of proteins combined with mass spectrometric detection of the extent and position of covalent modifications is a rapid, sensitive method for the study of protein structure and flexibility. By altering the pH of the solution, we have induced non-denaturing changes in the structure of bacterial ribosomal proteins and detected these conformational changes by covalent labeling. Changes in ribosomal protein modification across a pH range from 6.6 to 8.3 are unique to each protein, and correlate with their structural environment in the ribosome. Lysine residues whose extent of modification increases as a function of increasing pH are on the surface of proteins, but in close proximity either to glutamate and aspartate residues, or to rRNA backbone phosphates. Increasing pH disrupts tertiary and quaternary interactions mediated by hydrogen bonding or ionic interactions, and regions of protein structure whose conformations are sensitive to these changes are of potential importance in modulating the flexibility of the ribosome or its interaction with other cellular complexes.

The importance of ribosome production, and the 5S RNP-MDM2 pathway, in health and disease.

PubMed

Pelava, Andria; Schneider, Claudia; Watkins, Nicholas J

2016-08-15

Ribosomes are abundant, large RNA-protein complexes that are the source of all protein synthesis in the cell. The production of ribosomes is an extremely energetically expensive cellular process that has long been linked to human health and disease. More recently, it has been shown that ribosome biogenesis is intimately linked to multiple cellular signalling pathways and that defects in ribosome production can lead to a wide variety of human diseases. Furthermore, changes in ribosome production in response to nutrient levels in the diet lead to metabolic re-programming of the liver. Reduced or abnormal ribosome production in response to cellular stress or mutations in genes encoding factors critical for ribosome biogenesis causes the activation of the tumour suppressor p53, which leads to re-programming of cellular transcription. The ribosomal assembly intermediate 5S RNP (ribonucleoprotein particle), containing RPL5, RPL11 and the 5S rRNA, accumulates when ribosome biogenesis is blocked. The excess 5S RNP binds to murine double minute 2 (MDM2), the main p53-suppressor in the cell, inhibiting its function and leading to p53 activation. Here, we discuss the involvement of ribosome biogenesis in the homoeostasis of p53 in the cell and in human health and disease. © 2016 The Author(s).

Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis.

PubMed

Chen, Yanhong; Oba, Masahito; Guan, Le Luo

2012-10-12

In order to determine differences in the ruminal bacterial community and host Toll-like receptor (TLR) gene expression of beef cattle with different susceptibility to acidosis, rumen papillae and content were collected from acidosis-susceptible (AS, n=3) and acidosis-resistant (AR, n=3) steers. The ruminal bacterial community was characterized using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real time PCR (qRT-PCR) analysis. Global R analysis of bacterial profile similarity revealed that bacterial diversity was significantly different between AR and AS groups for both rumen content (P=0.001) and epithelial (P=0.002) communities. The copy number of total bacterial 16S rRNA genes in content of AS steers was 10-fold higher than that of AR steers, and the copy number of total 16S rRNA genes of epimural bacteria in AR steers was positively correlated with ruminal pH (r=0.59, P=0.04), and negatively correlated with total VFA concentration (r=-0.59, P=0.05). The expressions of host TLR2 and 4 genes were significantly higher in AR steers compared to those in AS steers. These findings enhance our understanding about the ruminal microbial ecology and host gene expression changes that may be useful in the prevention of ruminal acidosis. Copyright © 2012 Elsevier B.V. All rights reserved.

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

PubMed

Zuo, Yu; Xie, Wenfang; Pang, Yue; Li, Tiesong; Li, Qingwei; Li, Yingying

2017-01-01

The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

16S rRNA gene-based association study identified microbial taxa associated with pork intramuscular fat content in feces and cecum lumen.

PubMed

Fang, Shaoming; Xiong, Xingwei; Su, Ying; Huang, Lusheng; Chen, Congying

2017-07-19

Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improving the pork IMF. Gut microbiome plays an important role in host metabolism and energy harvest. Whether gut microbiota exerts effect on IMF remains unknown. In this study, we investigated the microbial community structure of 500 samples from porcine cecum and feces using high-throughput 16S rRNA gene sequencing. We found that phylogenetic composition and potential function capacity of microbiome varied between two types of samples. Bacteria wide association study identified 119 OTUs significantly associated with IMF in the two types of samples (FDR < 0.1). Most of the IMF-associated OTUs belong to the bacteria related to polysaccharide degradation and amino acid metabolism (such as Prevotella, Treponema, Bacteroides and Clostridium). Potential function capacities related to metabolisms of carbohydrate, energy and amino acids, cell motility, and membrane transport were significantly associated with IMF content. FishTaco analysis suggested that the shifts of potential function capacities of microbiome associated with IMF might be caused by the IMF-associated microbial taxa. This study firstly evaluated the contribution of gut microbiome to porcine IMF content. The results presented a potential capacity for improving IMF through modulating gut microbiota.

Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs

PubMed Central

Yip, W. S. Vincent; Shigematsu, Hideki; Taylor, David W.; Baserga, Susan J.

2016-01-01

Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2′-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture. PMID:27342279

Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk.

PubMed

Hantsis-Zacharov, Elionora; Shakéd, Tamar; Senderovich, Yigal; Halpern, Malka

2008-11-01

A Gram-negative, rod-shaped, oxidase-positive, aerobic, non-motile and orange-pigmented bacterial strain, containing flexirubin-type pigments, designated H8(T), was isolated from raw cow's milk in Israel. 16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Chryseobacterium (family Flavobacteriaceae, phylum Bacteroidetes). The levels of 16S rRNA gene sequence similarity between strain H8(T) and the type strains of described Chryseobacterium species were 97.5 % or lower. Strain H8(T) grew at 5-37 degrees C and with 0-3.0 % NaCl. The dominant cellular fatty acids were iso-15 : 0, iso-17 : 0 3-OH, iso-17 : 1omega9c and summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1omega7c). On the basis of phenotypic properties and phylogenetic distinctiveness, the milk isolate H8(T) is classified as a member of a novel species in the genus Chryseobacterium, for which the name Chryseobacterium oranimense sp. nov. (type strain H8(T) =LMG 24030(T) =DSM 19055(T)) is proposed.

Complete Mitochondrial Genome of the Medicinal Mushroom Ganoderma lucidum

PubMed Central

Chen, Haimei; Chen, Xiangdong; Lan, Jin; Liu, Chang

2013-01-01

Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the understanding of the functions and evolution of fungal mitochondrial DNA. PMID:23991034

Analysis of Gut Microbiota in Patients with Parkinson's Disease.

PubMed

Petrov, V A; Saltykova, I V; Zhukova, I A; Alifirova, V M; Zhukova, N G; Dorofeeva, Yu B; Tyakht, A V; Kovarsky, B A; Alekseev, D G; Kostryukova, E S; Mironova, Yu S; Izhboldina, O P; Nikitina, M A; Perevozchikova, T V; Fait, E A; Babenko, V V; Vakhitova, M T; Govorun, V M; Sazonov, A E

2017-04-01

Gut microbiota of patients with Parkinson's disease and healthy volunteers was analyzed by the method of high throughput 16S rRNA sequencing of bacterial genomes. In patients with Parkinson's diseases, changes in the content of 9 genera and 15 species of microorganisms were revealed: reduced content of Dorea, Bacteroides, Prevotella, Faecalibacterium, Bacteroides massiliensis, Stoquefichus massiliensis, Bacteroides coprocola, Blautia glucerasea, Dorea longicatena, Bacteroides dorei, Bacteroides plebeus, Prevotella copri, Coprococcus eutactus, and Ruminococcus callidus, and increased content of Christensenella, Catabacter, Lactobacillus, Oscillospira, Bifidobacterium, Christensenella minuta, Catabacter hongkongensis, Lactobacillus mucosae, Ruminococcus bromii, and Papillibacter cinnamivorans. This microbiological pattern of gut microflora can trigger local inflammation followed by aggregation of α-synuclein and generation of Lewy bodies.

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing.

PubMed

Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling; Chua, Yi-Heng; Goh, Kian Mau

2015-01-01

The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.

The influence of microwave radiation from cellular phone on fetal rat brain.

PubMed

Jing, Ji; Yuhua, Zhang; Xiao-qian, Yang; Rongping, Jiang; Dong-mei, Guo; Xi, Cui

2012-03-01

The increasing use of cellular phones in our society has brought focus on the potential detrimental effects to human health by microwave radiation. The aim of our study was to evaluate the intensity of oxidative stress and the level of neurotransmitters in the brains of fetal rats chronically exposed to cellular phones. The experiment was performed on pregnant rats exposed to different intensities of microwave radiation from cellular phones. Thirty-two pregnant rats were randomly divided into four groups: CG, GL, GM, and GH. CG accepted no microwave radiation, GL group radiated 10 min each time, GM group radiated 30 min, and GH group radiated 60 min. The 3 experimental groups were radiated 3 times a day from the first pregnant day for consecutively 20 days, and on the 21st day, the fetal rats were taken and then the contents of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), malondialdehyde (MDA), noradrenaline (NE), dopamine (DA), and 5-hydroxyindole acetic acid (5-HT) in the brain were assayed. Compared with CG, there were significant differences (P<0.05) found in the contents of SOD, GSH-Px, and MDA in GM and GH; the contents of SOD and GSH-Px decreased and the content of MDA increased. The significant content differences of NE and DA were found in fetal rat brains in GL and GH groups, with the GL group increased and the GH group decreased. Through this study, we concluded that receiving a certain period of microwave radiation from cellular phones during pregnancy has certain harm on fetal rat brains.

Anti-replicative recombinant 5S rRNA molecules can modulate the mtDNA heteroplasmy in a glucose-dependent manner.

PubMed

Loutre, Romuald; Heckel, Anne-Marie; Jeandard, Damien; Tarassov, Ivan; Entelis, Nina

2018-01-01

Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy. We have also shown that 5S ribosomal RNA, partially imported into human mitochondria, can be used as a vector to deliver anti-replicative oligoribonucleotides into human mitochondria. So far, the efficiency of cellular expression of recombinant 5S rRNA molecules bearing therapeutic insertions remained very low. In the present study, we designed new versions of anti-replicative recombinant 5S rRNA targeting a large deletion in mitochondrial DNA which causes the KSS syndrome, analyzed their specific annealing to KSS mitochondrial DNA and demonstrated their import into mitochondria of cultured human cells. To obtain an increased level of the recombinant 5S rRNA stable expression, we created transmitochondrial cybrid cell line bearing a site for Flp-recombinase and used this system for the recombinase-mediated integration of genes coding for the anti-replicative recombinant 5S rRNAs into nuclear genome. We demonstrated that stable expression of anti-replicative 5S rRNA versions in human transmitochondrial cybrid cells can induce a shift in heteroplasmy level of KSS mutation in mtDNA. This shift was directly dependent on the level of the recombinant 5S rRNA expression and the sequence of the anti-replicative insertion. Quantification of mtDNA copy number in transfected cells revealed the absence of a non-specific effect on wild type mtDNA replication, indicating that the decreased proportion between mutant and wild type mtDNA molecules is not a consequence of a random repopulation of depleted pool of mtDNA genomes. The heteroplasmy change could be also modulated by cell growth conditions, namely increased by cells culturing in a carbohydrate-free medium, thus forcing them to use oxidative phosphorylation and providing a selective advantage for cells with improved respiration capacities. We discuss the advantages and limitations of this approach and propose further development of the anti-replicative strategy based on the RNA import into human mitochondria.

Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-Proteobacteria.

PubMed

López-López, Arantxa; Pujalte, María J; Benlloch, Susana; Mata-Roig, Manuel; Rosselló-Mora, Ramón; Garay, Esperanza; Rodríguez-Valera, Francisco

2002-07-01

A novel bacterium from the Mediterranean Sea was isolated under oligotrophic conditions at in situ temperature after prolonged continuous culture. The isolates were initially characterized by partial 16S rRNA gene sequencing. Similarity searches of one of the isolates, QMT2T, indicated high sequence identity to the well-characterized Rhodospirillum rubrum, [Aquaspirillum] itersonii and [Oceanospirillum] pusillum micro-organisms, which are representatives of the alpha-subclass of the Proteobacteria. The highest level of similarity of the complete 165 rRNA gene with respect to these microorganisms was 89%. Features such as the low similarities of 165 rRNA of QMT2T with its phylogenetically close neighbours, the distinct G+C content, and the differences in phenotypic features, including pigmentation, fatty acid composition, salt tolerance, the lack of bacteriochlorophyll a, and the capacity to use carbohydrates as carbon sources, are indicative of the novel nature of the isolate QMT2T among the alpha-Proteobacteria. This report describes the classification of strain QMT2T (= DSM 14000T = CECT 5390T) as a new genus and species, Thalassospira lucentensis gen. nov, sp. nov., in the family Rhodospirillaceae.

Characterization and Screening of Native Scenedesmus sp. Isolates Suitable for Biofuel Feedstock

PubMed Central

Gour, Rakesh Singh; Chawla, Aseem; Singh, Harvinder; Chauhan, Rajinder Singh; Kant, Anil

2016-01-01

In current study isolates of two native microalgae species were screened on the basis of growth kinetics and lipid accumulation potential. On the basis of data obtained on growth parameters and lipid accumulation, it is concluded that Scenedesmus dimorphus has better potential as biofuel feedstock. Two of the isolates of Scenedesmus dimorphus performed better than other isolates with respect to important growth parameters with lipid content of ~30% of dry biomass. Scenedesmus dimorphus was found to be more suitable as biodiesel feedstock candidate on the basis of cumulative occurrence of five important biodiesel fatty acids, relative occurrence of SFA (53.04%), MUFA (23.81%) and PUFA (19.69%), and more importantly that of oleic acid in its total lipids. The morphological observations using light and Scanning Electron Microscope and molecular characterization using amplified 18S rRNA gene sequences of microalgae species under study were also performed. Amplified 18S rRNA gene fragments of the microalgae species were sequenced, annotated at the NCBI website and phylogenetic analysis was done. We have published eight 18S rRNA gene sequences of microalgae species in NCBI GenBank. PMID:27195694

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

Occurrence and characterization of hitherto unknown Streptomyces species in semi-arid soils.

PubMed

Kumar, Surendra; Priya, E; Singh Solanki, Dilip; Sharma, Ruchika; Gehlot, Praveen; Pathak, Rakesh; Singh, S K

2016-09-01

Streptomyces the predominant genus of Actinobacteria and plays an important role in the recycling of soil organic matter and production of important secondary metabolites. The occurrence and diversity assessment of Streptomyces species revealed alkaline and poor nutrient status of soils of semi-arid region of Jodhpur, Rajasthan. The morphological and biochemical characterization of 21 Streptomyces isolates facilitated Genus level identification but were insufficient to designate species. Species designation based on 16S rRNA gene delineated 21 isolates into 14 Streptomyces species. Upon BLAST search, the test isolates exhibited 98 to 100% identities with that of the best aligned sequences of the NCBI database. The GC content of 16S rRNA gene sequences of all the Streptomyces isolates tested ranged from 59.03% to 60.94%. The multiple sequence alignment of all the 21 Streptomyces isolates generated a phylogram with high bootstrap values indicating reliable grouping of isolates based on nucleotide sequence variations by way of insertion, deletion and substitutions and 16S rRNA length polymorphism. Some of the Streptomyces species molecularly identified under present study are reported for the first time from semi-arid region of Jodhpur.

Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov.

PubMed

Cai, Shichun; Dong, Xiuzhu

2010-04-01

An obligate anaerobic, Gram-staining-negative, mesophilic, cellulolytic bacterium, strain H1(T), was isolated from the rumen content of yak. Cells were straight to slightly curved rods, 0.8-1.0 x 3.0-4.0 microm in size, non-motile and encapsulated with mucous materials. Elliptical and terminal spores that swelled the cells were produced occasionally. The strain grew at 25-45 degrees C (optimum, 38 degrees C) and pH 6.0-7.8 (optimum, pH 6.7). Cellulose, cellobiose, xylan, xylose and maltose were used as carbon and energy sources, but not glucose. Products from cellulose and cellobiose fermentation were formic acid, acetic acid, carbon dioxide and trace amounts of ethanol, lactic acid and succinic acid. The genomic DNA G+C content was 33.7+/-1.2 mol%. The predominant fatty acids were C(16 : 0) (27.1 %), C(14 : 0) (9.2 %) and iso-C( 16 : 0) (6.4%). Based on the 16S rRNA gene sequence analysis, strain H1(T) was affiliated to the clostridial rRNA cluster XIVb and showed the highest 16S rRNA gene sequence similarity to Clostridium lentocellum DSM 5427(T) (96.0 %). These two strains formed a distinct lineage of the family 'Lachnospiraceae '. Based on data from this polyphasic taxonomic study, a new genus, Cellulosilyticum gen. nov., is proposed. Cellulosilyticum ruminicola sp. nov. is proposed for strain H1(T). The type strain of Cellulosilyticum ruminicola sp. nov. is strain H1(T) (=CGMCC 1.5065(T)=JCM 14822(T)). Clostridium lentocellum was reclassified in the new genus as Cellulosilyticum lentocellum comb. nov. (type strain RHM5(T)=ATCC 49066( T)=DSM 5427(T)=NCIMB 11756(T)).

Genome-Based Taxonomic Classification of Bacteroidetes

DOE PAGES

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; ...

2016-12-20

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Genome-Based Taxonomic Classification of Bacteroidetes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Genome-Based Taxonomic Classification of Bacteroidetes

PubMed Central

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter; Göker, Markus

2016-01-01

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved. PMID:28066339

The complete mitochondrial genome of the invasive Africanized Honey Bee, Apis mellifera scutellata (Insecta: Hymenoptera: Apidae).

PubMed

Gibson, Joshua D; Hunt, Greg J

2016-01-01

The complete mitochondrial genome from an Africanized honey bee population (AHB, derived from Apis mellifera scutellata) was assembled and analyzed. The mitogenome is 16,411 bp long and contains the same gene repertoire and gene order as the European honey bee (13 protein coding genes, 22 tRNA genes and 2 rRNA genes). ND4 appears to use an alternate start codon and the long rRNA gene is 48 bp shorter in AHB due to a deletion in a terminal AT dinucleotide repeat. The dihydrouracil arm is missing from tRNA-Ser (AGN) and tRNA-Glu is missing the TV loop. The A + T content is comparable to the European honey bee (84.7%), which increases to 95% for the 3rd position in the protein coding genes.

The ribosome as a missing link in the evolution of life.

PubMed

Root-Bernstein, Meredith; Root-Bernstein, Robert

2015-02-21

Many steps in the evolution of cellular life are still mysterious. We suggest that the ribosome may represent one important missing link between compositional (or metabolism-first), RNA-world (or genes-first) and cellular (last universal common ancestor) approaches to the evolution of cells. We present evidence that the entire set of transfer RNAs for all twenty amino acids are encoded in both the 16S and 23S rRNAs of Escherichia coli K12; that nucleotide sequences that could encode key fragments of ribosomal proteins, polymerases, ligases, synthetases, and phosphatases are to be found in each of the six possible reading frames of the 16S and 23S rRNAs; and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. Ribosomal RNA, in short, is not just a structural scaffold for proteins, but the vestigial remnant of a primordial genome that may have encoded a self-organizing, self-replicating, auto-catalytic intermediary between macromolecules and cellular life. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evidence for a close phylogenetic relationship between Melissococcus pluton, the causative agent of European foulbrood disease, and the genus Enterococcus.

PubMed

Cai, J; Collins, M D

1994-04-01

The 16S rRNA gene sequence of Melissococcus pluton, the causative agent of European foulbrood disease, was determined in order to investigate the phylogenetic relationships between this organism and other low-G + C-content gram-positive bacteria. A comparative sequence analysis revealed that M. pluton is a close phylogenetic relative of the genus Enterococcus.

Configuration of a high-content imaging platform for hit identification and pharmacological assessment of JMJD3 demethylase enzyme inhibitors.

PubMed

Mulji, Alpa; Haslam, Carl; Brown, Fiona; Randle, Rebecca; Karamshi, Bhumika; Smith, Julia; Eagle, Robert; Munoz-Muriedas, Jordi; Taylor, Joanna; Sheikh, Arshad; Bridges, Angela; Gill, Kirsty; Jepras, Rob; Smee, Penny; Barker, Mike; Woodrow, Mike; Liddle, John; Thomas, Pamela; Jones, Emma; Gordon, Laurie; Tanner, Rob; Leveridge, Melanie; Hutchinson, Sue; Martin, Margaret; Brown, Murray; Kruidenier, Laurens; Katso, Roy

2012-01-01

The biological complexity associated with the regulation of histone demethylases makes it desirable to configure a cellular mechanistic assay format that simultaneously encompasses as many of the relevant cellular processes as possible. In this report, the authors describe the configuration of a JMJD3 high-content cellular mechanistic imaging assay that uses single-cell multiparameter measurements to accurately assess cellular viability and the enzyme-dependent demethylation of the H3K27(Me)3 mark by exogenously expressed JMJD3. This approach couples robust statistical analyses with the spatial resolving power of cellular imaging. This enables segregation of expressing and nonexpressing cells into discrete subpopulations and consequently pharmacological quantification of compounds of interest in the expressing population at varying JMJD3 expression levels. Moreover, the authors demonstrate the utility of this hit identification strategy through the successful prosecution of a medium-throughput focused campaign of an 87 500-compound file, which has enabled the identification of JMJD3 cellular-active chemotypes. This study represents the first report of a demethylase high-content imaging assay with the ability to capture a repertoire of pharmacological tools, which are likely both to inform our mechanistic understanding of how JMJD3 is modulated and, more important, to contribute to the identification of novel therapeutic modalities for this demethylase enzyme.

Corynebacterium godavarianum sp. nov., isolated from the Godavari river, India.

PubMed

Jani, Kunal; Khare, Kaustubh; Senik, Svetlana; Karodi, Prachi; Vemuluri, Venkata Ramana; Bandal, Jayashree; Shouche, Yogesh; Rale, Vinay; Sharma, Avinash

2018-01-01

A Gram-stain-positive, rod-shaped, non-motile bacterium, strain PRD07 T , was isolated from Godavari river, India during the world's largest spiritual and religious mass bathing event 'Kumbh Mela'. Molecular analysis using 16S rRNA gene sequencing and phylogenetic analysis reveals the distinct phylogenetic positioning of strain PRD07 T within the genus Corynebacterium. The strain demonstrated highest sequence similarity to Corynebacterium imitans DSM 44264 T (97.9 %), Corynebacterium appendicis DSM 44531 T (97.1 %) and <96.7 % with all other members of the genus Corynebacterium. The G+C content of PRD07 T was 68.5 mol% (Tm) and the DNA-DNA hybridization depicts 61.09 % genomic relatedness with C. imitans DSM 44264 T . Chemotaxonomic assessment of strain PRD07 T suggested presence of C16 : 0 (31.6 %), C18 : 0 (3.5 %) and C18 : 1ω9c (58.6 %) as the major cellular fatty acids. The major polar lipids of strain PRD07 T were phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. Differentiating molecular, phylogenetic and chemotaxonomic characteristics of strain PRD07 T with its closest relatives necessitated the description of strain PRD07 T as a novel species of genus Corynebacterium for which the name Corynebacteriumgodavarianum sp. nov., has been proposed. The type strain is PRD07 T (=MCC 3388 T =KCTC 39803 T =LMG 29598 T ).

Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory.

PubMed

Ye, Xiao-Mei; Chu, Cui-Wei; Shi, Chao; Zhu, Jian-Chun; He, Qin; He, Jian

2015-03-01

Strain BUT-8(T), a Gram-stain-negative, non-motile and rod-shaped aerobic bacterium, was isolated from the activated sludge of a herbicide-manufacturing wastewater treatment facility. Comparative 16S rRNA gene sequence analysis revealed that strain BUT-8(T) clustered with species of the genus Lysobacter and was closely related to Lysobacter ruishenii DSM 22393(T) (98.3 %) and Lysobacter daejeonensis KACC 11406(T) (98.7 %). The DNA G+C content of the genomic DNA was 70.6 mol%. The major respiratory quinone was ubiquinone-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 010-methyl). The DNA-DNA relatedness between strain BUT-8(T) and its closest phylogenetic neighbours was below 70 %. Phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain BUT-8(T) belongs to the genus Lysobacter and represents a novel species for which the name Lysobacter caeni sp. nov. is proposed. The type strain is BUT-8(T) ( = CCTCC AB 2013087(T) = KACC 17141(T)). © 2015 IUMS.

Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits.

PubMed

Chen, Yi-Sheng; Wang, Li-Ting; Liao, Yu-Jou; Lan, Yi-Shan; Chang, Chi-Huan; Chang, Yu-Chung; Wu, Hui-Chung; Lo, Huei-Yin; Otoguro, Misa; Yanagida, Fujitoshi

2017-12-01

Two Gram-stain-positive, catalase-negative, rod-shaped, bacterial strains (313 T and 311) were isolated from banana fruits in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the highest similarity to both strains corresponded to the type strain of Lactobacillus nantensis (99.19 %), followed by Lactobacillus crustorum (98.99 %), Lactobacillus heilongjiangensis (98.59 %) and Lactobacillus farciminis (98.52 %). Phylogenetic analysis based on the sequences of two housekeeping genes, pheS and rpoA, revealed that these two strains were well separated from the Lactobacillus reference strains. DNA-DNA relatedness values revealed genotype separation of the two strains from the above four species. The DNA G+C content of strain 313 T was 35.5 mol%. The strains were homofermentative and mainly produced l-lactic acid from glucose. The major cellular fatty acids of strain 313 T were 18 : 1ω6c and/or 18 : 1ω7c, 16 : 0, and 19 : 1ω6c and/or 19 : 0 cyclo ω10c. Based on their physiological and genotypic characteristics, the isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillusmusae sp. nov. is proposed. The type strain is 313 T =NBRC 112868 T =BCRC 81020 T ).

Prevotella fusca sp. nov. and Prevotella scopos sp. nov., isolated from the human oral cavity.

PubMed

Downes, Julia; Wade, William G

2011-04-01

Two strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to belong to two separate taxa. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that the strains were both related to, but distinct from, the type strain of Prevotella melaninogenica. Two novel species, Prevotella fusca sp. nov. and Prevotella scopos sp. nov., are proposed to accommodate these strains. Both strains were saccharolytic and produced acetic and succinic acids, with lesser amounts of lactic and isovaleric acids, as end products of fermentation, and both were sensitive to 20 % bile. The principal cellular long-chain fatty acids of both strains were ai-C(15 : 0), 3-OH i-C(17 : 0), 3-OH C(16 : 0), i-C(15 : 0) and C(16 : 0). The DNA G+C contents of the type strains of Prevotella fusca (W1435(T)  = DSM 22504(T)  = CCUG 57946(T)) and Prevotella scopos (W2052(T)  = DSM 22613(T ) = CCUG 57945(T)) were 43 and 41 mol%, respectively. The two species could be differentiated by gelatin hydrolysis, cellobiose and ribose fermentation, and production of β-glucosidase.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

PubMed

Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

Aureimonas glaciistagni sp. nov., isolated from a melt pond on Arctic sea ice.

PubMed

Cho, Yirang; Lee, Inae; Yang, Yoon Y; Baek, Kiwoon; Yoon, Soo J; Lee, Yung M; Kang, Sung-Ho; Lee, Hong K; Hwang, Chung Y

2015-10-01

A Gram-staining-negative, motile, aerobic and rod-shaped bacterial strain, PAMC 27157T, was isolated from a melt pond on sea ice in the Chukchi Sea. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 27157T revealed an affiliation to the genus Aureimonas with the closest sequence similarity (96.2 %) to that of Aureimonas phyllosphaerae. Strain PAMC 27157T grew optimally at 30 °C and pH 7.0 in the presence of 3.5 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, sulfoquinovosyldiacylglycerol and an unidentified aminolipid. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 83.1 %) and the major respiratory quinone was Q-10. The genomic DNA G+C content was 69.1 mol%. The combined phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 27157T could be clearly distinguished from species of the genus Aureimonas with validly published names. Thus, strain PAMC 27157T should be classified as representing a novel species in the genus Aureimonas, for which the name Aureimonas glaciistagni sp. nov. is proposed. The type strain is PAMC 27157T ( = KCCM 43049T = JCM 30183T).

Streptomyces krungchingensis sp. nov., isolated from soil.

PubMed

Sripreechasak, Paranee; Phongsopitanun, Wongsakorn; Tamura, Tomohiko; Tanasupawat, Somboon

2017-01-01

A novel actinomycete, designated strain KC-035T, was isolated from soil collected from Krung Ching Waterfall National Park, Nakhon Si Thammarat Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological and chemotaxonomic properties typical of members of the genus Streptomyces: flexuous spore chain; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H6) and MK-9(H4) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as phospholipids; anteiso-C15 : 0, C16 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 as major cellular fatty acids; and DNA G+C content of 72 mol%. 16S rRNA gene sequence analysis revealed that strain KC-035T showed high similarity to Streptomyces albiflavescens n20T (99.16 %) and Streptomyces siamensis KC-038T (98.43 %) as well as formed a monophyletic clade with them in the phylogenetic tree. On the basis of comparison of phenotypic properties and the low level of DNA-DNA relatedness, strain KC-035T could be distinguished from its closely related Streptomyces species and is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces krungchingensis sp. nov. is proposed. The type strain is KC-035T (=NBRC 110087T=KCTC 29503T=TISTR 2402T).

Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus.

PubMed

Han, Ji-Hye; Kim, Tae-Su; Joung, Yochan; Kim, Seung Bum

2015-12-01

A Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90 %, while levels of similarity to other related taxa were less than 93.08 %. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15 : 1 G, iso-C15 : 0 and a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0 mol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T ( = KCTC 42060T = JCM 19844T).

Micrococcus endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots.

PubMed

Chen, Hua-Hong; Zhao, Guo-Zhen; Park, Dong-Jin; Zhang, Yu-Qin; Xu, Li-Hua; Lee, Jae-Chan; Kim, Chang-Jin; Li, Wen-Jun

2009-05-01

A Gram-positive bacterial strain, designated YIM 56238(T), was isolated from plant roots (Aquilaria sinensis), and characterized by using a polyphasic approach. Strain YIM 56238(T) grew optimally at pH 7.0-8.0 and at 28 degrees C. Analysis of the 16S rRNA gene sequence of strain YIM 56238(T) indicated that it belongs to the genus Micrococcus. Chemotaxonomic data strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine and glycine; the predominant menaquinones were MK-8(H(2)) (63.6 %) and MK-7(H(2)) (21.1 %); the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid; and the major cellular fatty acids were iso-C(15 : 0) (30.95 %) and anteiso-C(15 : 0) (53.75 %). The G+C content of the genomic DNA was 72.9 mol%. A number of physiological features were found that clearly distinguished strain YIM 56238(T) from recognized species of the genus Micrococcus. DNA-DNA hybridization studies suggested that the novel strain represents a separate genomic species. On the basis of the data, therefore, strain YIM 56238(T) represents a novel species of the genus Micrococcus, for which the name Micrococcus endophyticus sp. nov. is proposed. The type strain is YIM 56238(T) (=DSM 17945(T)=KCTC 19156(T)).

Rhabdobacter roseus gen. nov., sp. nov., isolated from soil.

PubMed

Dahal, Ram Hari; Kim, Jaisoo

2016-01-01

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium, designated strain R49T, was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R49T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes that was distinct from the most closely related genera Dyadobacter (91.98-93.85 % sequence similarity), Persicitalea (88.69 %) and Runella (84.79-85.81 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain R49T was 53.9 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R49T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhabdobacter roseus gen. nov., sp. nov. is proposed. The type strain of Rhabdobacter roseus is R49T ( = KEMB 9005-318T = KACC 18395T = JCM 30685T).

Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

PubMed Central

Rahman, Raja Noor Zaliha Raja Abd; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

2007-01-01

Background Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Results Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70°C and was also stable up to 60°C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). Conclusion Strain T1T was able to secrete extracellular thermostable lipase into culture medium. The strain T1T was identified as Geobacillus zalihae T1T as it differs from its type strains Geobacillus kaustophilus (DSM 7263T) and Geobacillus thermoleovorans (DSM 5366T) on some physiological studies, cellular fatty acids composition, RiboPrint analysis, length of lipase gene and protein profile. PMID:17692114

Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia.

PubMed

Abd Rahman, Raja Noor Zaliha Raja; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

2007-08-10

Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78 degrees C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5-99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70 degrees C and was also stable up to 60 degrees C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). Strain T1T was able to secrete extracellular thermostable lipase into culture medium. The strain T1T was identified as Geobacillus zalihae T1T as it differs from its type strains Geobacillus kaustophilus (DSM 7263T) and Geobacillus thermoleovorans (DSM 5366T) on some physiological studies, cellular fatty acids composition, RiboPrint analysis, length of lipase gene and protein profile.

Geodermatophilus tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert.

PubMed

Montero-Calasanz, Maria del Carmen; Göker, Markus; Broughton, William J; Cattaneo, Arlette; Favet, Jocelyne; Pötter, Gabriele; Rohde, Manfred; Spröer, Cathrin; Schumann, Peter; Klenk, Hans-Peter; Gorbushina, Anna A

2013-05-01

Three novel Gram-positive, aerobic, actinobacterial strains, CF5/2(T), CF5/1 and CF7/1, were isolated in 2007 during environmental screening of arid desert soil in the Sahara desert, Chad. Results from riboprinting, MALDI-TOF protein spectra and 16S rRNA sequence analysis confirmed that all three strains belonged to the same species. Phylogenetic analysis of 16S rRNA sequences with the strains' closest relatives indicated that they represented a distinct species. The three novel strains also shared a number of physiological and biochemical characteristics distinct from previously named Geodermatophilus species. The novel strains' peptidoglycan contained meso-diaminopimelic acid; their main phospholipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and a small amount of phosphatidylglycerol; MK-9(H4) was the dominant menaquinone. The major cellular fatty acids were the branched-chain saturated acids iso-C16:0 and iso-C15:0. Galactose was detected as diagnostic sugar. Based on these chemotaxonomic results, 16S rRNA gene sequence analysis and DNA-DNA hybridization between strain CF5/2(T) and the type strains of Geodermatophilus saharensis, Geodermatophilus arenarius, Geodermatophilus nigrescens, Geodermatophilus telluris and Geodermatophilus siccatus, the isolates CF5/2(T), CF5/1 and CF7/1 are proposed to represent a novel species, Geodermatophilus tzadiensis, with type strain CF5/2(T)=DSM 45416=MTCC 11411 and two reference strains, CF5/1 (DSM 45415) and CF7/1 (DSM 45420). Copyright © 2013 Elsevier GmbH. All rights reserved.

Ribosomal RNA maturation in Schizosaccharomyces pombe is dependent on a large ribonucleoprotein complex of the internal transcribed spacer 1.

PubMed

Lalev, A I; Abeyrathne, P D; Nazar, R N

2000-09-08

The interdependency of steps in the processing of pre-rRNA in Schizosaccharomyces pombe suggests that RNA processing, at least in part, acts as a quality control mechanism which helps assure that only functional RNA is incorporated into mature ribosomes. To determine further the role of the transcribed spacer regions in rRNA processing and to detect interactions which underlie the interdependencies, the ITS1 sequence was examined for its ability to form ribonucleoprotein complexes with cellular proteins. When incubated with protein extract, the spacer formed a specific large RNP. This complex was stable to fractionation by agarose or polyacrylamide gel electrophoresis. Modification exclusion analyses indicated that the proteins interact with a helical domain which is conserved in the internal transcribed spacers. Mutagenic analyses confirmed an interaction with this sequence and indicated that this domain is critical to the efficient maturation of the precursor RNA. The protein constituents, purified by affinity chromatography using the ITS1 sequence, retained an ability to form stable RNP. Protein analyses of gel purified complex, prepared with affinity-purified proteins, indicated at least 20 protein components ranging in size from 20-200 kDa. Peptide mapping by Maldi-Toff mass spectroscopy identified eight hypothetical RNA binding proteins which included four different RNA-binding motifs. Another protein was putatively identified as a pseudouridylate synthase. Additional RNA constituents were not detected. The significance of this complex with respect to rRNA maturation and interdependence in rRNA processing is discussed. Copyright 2000 Academic Press.

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes ▿ †

PubMed Central

Will, Christiane; Thürmer, Andrea; Wollherr, Antje; Nacke, Heiko; Herold, Nadine; Schrumpf, Marion; Gutknecht, Jessica; Wubet, Tesfaye; Buscot, François; Daniel, Rolf

2010-01-01

The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H′) was higher in the A horizons than in the corresponding B horizons. In addition, the H′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass. PMID:20729324

Anaerobium acetethylicum gen. nov., sp. nov., a strictly anaerobic, gluconate-fermenting bacterium isolated from a methanogenic bioreactor.

PubMed

Patil, Yogita; Junghare, Madan; Pester, Michael; Müller, Nicolai; Schink, Bernhard

2015-10-01

A novel strictly anaerobic, mesophilic bacterium was enriched and isolated with gluconate as sole substrate from a methanogenic sludge collected from a biogas reactor. Cells of strain GluBS11T stained Gram-positive and were non-motile, straight rods, measuring 3.0-4.5 × 0.8-1.2 μm. The temperature range for growth was 15-37 °C, with optimal growth at 30 °C, the pH range was 6.5-8.5, with optimal growth at pH 7, and the generation time under optimal conditions was 60 min. API Rapid 32A reactions were positive for α-galactosidase, α-glucosidase and β-glucosidase and negative for catalase and oxidase. A broad variety of substrates was utilized, including gluconate, glucose, fructose, maltose, sucrose, lactose, galactose, melezitose, melibiose, mannitol, erythritol, glycerol and aesculin. Products of gluconate fermentation were ethanol, acetate, formate, H2 and CO2. Neither sulfate nor nitrate served as an electron acceptor. Predominant cellular fatty acids (>10 %) were C14 : 0, C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH and C18 : 1ω7c. The DNA G+C content of strain GluBS11T was 44.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data revealed that strain GluBS11T is a member of subcluster XIVa within the order Clostridiales. The closest cultured relatives are Clostridium herbivorans (93.1 % similarity to the type strain), Clostridium populeti (93.3 %), Eubacterium uniforme (92.4 %) and Clostridium polysaccharolyticum (91.5 %). Based on this 16S rRNA gene sequence divergence (>6.5 %) as well as on chemotaxonomic and phenotypic differences from these taxa, strain GluBS11T is considered to represent a novel genus and species, for which the name Anaerobium acetethylicum gen. nov., sp. nov. is proposed. The type strain of Anaerobium acetethylicum is GluBS11T ( = LMG 28619T = KCTC 15450T = DSM 29698T).

Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system.

PubMed

Liu, Ying; Liu, Liang-Zi; Zhong, Zhi-Ping; Zhou, Yu-Guang; Liu, Ying; Liu, Zhi-Pei

2014-12-01

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated S1(T), was isolated from the Cynoglossus semilaevis culture pond in a recirculating mariculture system in Tianjin, China. The taxonomy of strain S1(T) was studied by using a polyphasic approach. Cells of strain S1(T) were non-spore-forming, curved rods, 0.4-0.6 µm wide and 1.2-2.0 µm long, and motile by means of a single polar flagellum. The strain was positive for oxidase and catalase activities. Strain S1(T) was able to grow at 4-30 °C (optimum, 25 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.5) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain S1(T) contained Q-8 as the sole respiratory quinone and C16 : 1ω7c/C16 : 1ω6c and C16 : 0 as the predominant cellular fatty acids. The genomic DNA G+C content was 40.1 mol% (Tm). Phylogenetic analysis based on 16S rRNA gene sequences placed strain S1(T) in the genus Colwellia, and it formed a distinct lineage in the phylogenetic tree together with Colwellia meonggei MA1-3(T), Colwellia aestuarii SMK-10(T), Colwellia polaris 537(T) and Colwellia chukchiensis BCw111(T), with 97.7, 96.1, 95.9 and 95.0 % 16S rRNA gene sequence similarity to these strains, respectively. DNA-DNA relatedness of strain S1(T) to Colwellia meonggei MA1-3(T) was 23.5±3.6 %. On the basis of the phylogenetic and phenotypic evidence, strain S1(T) is considered to represent a novel species of the genus Colwellia, for which the name Colwellia aquaemaris sp. nov. is proposed. The type strain is S1(T) ( = CGMCC 1.12165(T) = JCM 18479(T)). © 2014 IUMS.

Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.

PubMed

Finster, Kai W; Kjeldsen, Kasper U

2010-03-01

Two deltaproteobacterial sulfate reducers, designated strain I.8.1(T) and I.9.1(T), were isolated from the oxygen minimum zone water column off the coast of Peru at 400 and 500 m water depth. The strains were Gram-negative, vibrio-shaped and motile. Both strains were psychrotolerant, grew optimally at 20 degrees C at pH 7.0-8.0 and at 2.5-3.5% NaCl (w/v). The strains grew by utilizing hydrogen/acetate, C(3-4) fatty acids, amino acids and glycerol as electron acceptors for sulfate reduction. Fumarate, lactate and pyruvate supported fermentative growth. Sulfate, sulfite, thiosulfate and taurin supported growth as electron acceptors. Both strains were catalase-positive and highly oxygen-tolerant, surviving 24 days of exposure to atmospheric concentrations. MK6 was the only respiratory quinone. The most prominent cellular fatty acid was iso-17:1-omega9c (18%) for strain I.8.1(T) and iso-17:0-omega9c (14%) for strain I.9.1(T). The G+C contents of their genomic DNA were 45-46 mol%. Phylogenetic analysis of 16S rRNA and dsrAB gene sequences showed that both strains belong to the genus Desulfovibrio. Desulfovibrio acrylicus DSM 10141(T) and Desulfovibrio marinisediminis JCM 14577(T) represented their closest validly described relatives with pairwise 16S rRNA gene sequence identities of 98-99%. The level of DNA-DNA hybridization between strains I.8.1(T) and I.9.1(T) was 30-38%. The two strains shared 10-26% DNA-DNA relatedness with D. acrylicus. Based on a polyphasic investigation it is proposed that strains I.8.1(T) and I.9.1(T) represent a novel species for which the name Desulfovibrio oceani sp. nov. is proposed with the two subspecies D. oceani subsp. oceani (type strain, I.8.1(T) = DSM 21390(T) = JCM 15970(T)) and D. oceani subsp. galateae (type strain, I.9.1(T) = DSM 21391(T) = JCM 15971(T)).

Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka.

PubMed

Behera, Pratiksha; Venkata Ramana, V; Maharana, Bhagirathi; Joseph, Neetha; Vaishampayan, Parag; Singh, Nitin K; Shouche, Yogesh; Bhadury, Punyasloke; Mishra, Samir R; Raina, Vishakha; Suar, Mrutyunjay; Pattnaik, Ajit K; Rastogi, Gurdeep

2017-05-01

A facultatively anaerobic, Gram-stain-negative, rod-shaped, nitrogen-fixing, endophytic bacterial strain designated MP23T was isolated from the roots of Phragmites karka growing in Chilika Lagoon, Odisha, India. Strain MP23T was slightly halophilic, and the optimal NaCl concentration and temperature for growth were 1 % and 30 °C, respectively. On the basis of 16S rRNA gene sequence similarities, strain MP23T was affiliated to the family Enterobacteriaceae and most closely related to Mangrovibacter yixingensis KCTC 42181T and Mangrovibacter plantisponsor DSM 19579T with 99.71 % similarity, followed by Salmonella enterica subsp. salamae DSM 9220T (97.22 %), Cronobacter condimenti LMG 26250T (97.14 %) and Salmonella enterica subsp. diarizonae DSM 14847T (97 %). Sequence analysis of 16S rRNA, hsp60, gyrB and rpoB genes showed that strain MP23T formed a phylogenetic cluster with M. yixingensis KCTC 42181T and M. plantisponsor DSM 19579T indicating that it belongs to the genus Mangrovibacter. The major cellular fatty acids were C16 : 0, C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C14 : 0, C14 : 0 3-OH and/or iso-C16 : 1 I and C17 : 0 cyclo. Polar lipids of strain MP23T consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 50.3 mol%. Based on experimental DNA-DNA hybridization values and average nucleotide identity derived from in silico comparison of whole-genome sequences, strain MP23T could be distinguished from its closest neighbours. We therefore conclude that strain MP23T represents a novel species of the genus Mangrovibacter for which the name Mangrovibacter phragmitis sp. nov. is proposed. The type strain is MP23T (=DSM 100250T=KCTC 42580T).

Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, Catriona, E-mail: catriona.kelly@qub.ac.uk; Flatt, Peter R.; McClenaghan, Neville H.

2010-08-20

Research highlights: {yields} TGP52 cells display enhanced functionality in pseudoislet form. {yields} Somatostatin content was reduced, but secretion increased in high glucose conditions. {yields} Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mMmore » glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.« less

Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste.

PubMed

Angenent, Largus T; Sung, Shihwu; Raskin, Lutgarde

2002-11-01

Changes in methanogenic population levels were followed during startup of a full-scale, farm-based anaerobic sequencing batch reactor (ASBR) and these changes were linked to operational and performance data. The ASBR was inoculated with anaerobic digester sludge from a municipal wastewater treatment facility. During an acclimation period of approximately 3 months, the ASBR content was diluted to maintain a total ammonia-N level of approximately 2000mg l(-1). After this acclimation period, the volatile solids loading rate was increased to its design value of 1.7g l(-1) day(-1) with a 15-day hydraulic retention time, which increased the total ammonia-N level in the ASBR to approximately 3,600 mg l(-1). The 16S ribosomal RNA (rRNA) levels of the acetate-utilizing methanogens of the genus Methanosarcina decreased from 3.8% to 1.2% (expressed as a percentage of the total 16S rRNA levels) during this period, while the 16S rRNA levels of Methanosaeta concilii remained low (below 2.2%). Methane production and reactor performance were not affected as the 16S rRNA levels of the hydrogen-utilizing methanogens of the order Methanomicrobiales increased from 2.3% to 7.0%. Hence, it is likely that during operation with high ammonia levels, the major route of methane production is through a syntrophic relationship between acetate-oxidizing bacteria and hydrogen-utilizing methanogens. Anaerobic digestion at total ammonia-N levels exceeding 3500mg l(-1) was sustainable apparently due to the acclimation of hydrogen-utilizing methanogens to high ammonia levels.

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

PubMed Central

Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling; Chua, Yi-Heng; Goh, Kian Mau

2015-01-01

The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community. PMID:25798135

Small nucleoli are a cellular hallmark of longevity

PubMed Central

Tiku, Varnesh; Jain, Chirag; Raz, Yotam; Nakamura, Shuhei; Heestand, Bree; Liu, Wei; Späth, Martin; Suchiman, H. Eka. D.; Müller, Roman-Ulrich; Slagboom, P. Eline; Partridge, Linda; Antebi, Adam

2017-01-01

Animal lifespan is regulated by conserved metabolic signalling pathways and specific transcription factors, but whether these pathways affect common downstream mechanisms remains largely elusive. Here we show that NCL-1/TRIM2/Brat tumour suppressor extends lifespan and limits nucleolar size in the major C. elegans longevity pathways, as part of a convergent mechanism focused on the nucleolus. Long-lived animals representing distinct longevity pathways exhibit small nucleoli, and decreased expression of rRNA, ribosomal proteins, and the nucleolar protein fibrillarin, dependent on NCL-1. Knockdown of fibrillarin also reduces nucleolar size and extends lifespan. Among wildtype C. elegans, individual nucleolar size varies, but is highly predictive for longevity. Long-lived dietary restricted fruit flies and insulin-like-peptide mutants exhibit small nucleoli and fibrillarin expression, as do long-lived dietary restricted and IRS1 knockout mice. Furthermore, human muscle biopsies from individuals who underwent modest dietary restriction coupled with exercise also display small nucleoli. We suggest that small nucleoli are a cellular hallmark of longevity and metabolic health conserved across taxa. PMID:28853436

Small nucleoli are a cellular hallmark of longevity.

PubMed

Tiku, Varnesh; Jain, Chirag; Raz, Yotam; Nakamura, Shuhei; Heestand, Bree; Liu, Wei; Späth, Martin; Suchiman, H Eka D; Müller, Roman-Ulrich; Slagboom, P Eline; Partridge, Linda; Antebi, Adam

2016-08-30

Animal lifespan is regulated by conserved metabolic signalling pathways and specific transcription factors, but whether these pathways affect common downstream mechanisms remains largely elusive. Here we show that NCL-1/TRIM2/Brat tumour suppressor extends lifespan and limits nucleolar size in the major C. elegans longevity pathways, as part of a convergent mechanism focused on the nucleolus. Long-lived animals representing distinct longevity pathways exhibit small nucleoli, and decreased expression of rRNA, ribosomal proteins, and the nucleolar protein fibrillarin, dependent on NCL-1. Knockdown of fibrillarin also reduces nucleolar size and extends lifespan. Among wildtype C. elegans, individual nucleolar size varies, but is highly predictive for longevity. Long-lived dietary restricted fruit flies and insulin-like-peptide mutants exhibit small nucleoli and fibrillarin expression, as do long-lived dietary restricted and IRS1 knockout mice. Furthermore, human muscle biopsies from individuals who underwent modest dietary restriction coupled with exercise also display small nucleoli. We suggest that small nucleoli are a cellular hallmark of longevity and metabolic health conserved across taxa.

Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.

PubMed

Kaur, Sukhpreet; Yawar, Mir; Kumar, P Anil; Suresh, K

2014-03-01

A Gram-stain-positive, rod-shaped, spore-forming and strictly anaerobic bacterium, designated UB-B.2(T), was isolated from an industrial effluent anaerobic digester sample. It grew optimally at 30 °C and pH 7.0. Comparative analysis of the 16S rRNA gene sequence confirmed that strain UB-B.2(T) was closely related to Clostridium hathewayi DSM 13479(T) (97.84% similarity), a member of rRNA gene cluster XIVa of the genus Clostridium, and formed a coherent cluster with other related members of the Blautia (Clostridium) coccoides rRNA group in phylogenetic analyses. The end products of glucose fermentation by strain UB-B.2(T) were acetate and propionate. The G+C content of the DNA was 51.4 mol%. Although strain UB-B.2(T) showed 97.8% 16S rRNA gene sequence identity to the type strain of C. hathewayi, it exhibited only 38.4% relatedness at the whole-genome level. It also showed differences from its closest phylogenetic relative, C. hathewayi DSM 13479(T), in phenotypic characteristics such as hydrolysis of aesculin, starch and urea and fermentation end products. Both strains showed phenotypic differences from the members of rRNA gene cluster XIVa of the genus Clostridium. Based on these differences, C. hathewayi DSM 13479(T) and strain UB-B.2(T) were identified as representatives of a new genus of the family Clostridiaceae. Thus, we propose the reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov., the type species of the new genus (type strain DSM 13479(T) = CCUG 43506(T) = MTCC 10951(T)). Strain UB-B.2(T) ( = MTCC 11101(T) = DSM 24995(T)) is assigned to the novel species Hungatella effluvii gen. nov., sp. nov as the type strain.

The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome

PubMed Central

Nedelcu, Aurora M.; Lee, Robert W.; Lemieux, Claude; Gray, Michael W.; Burger, Gertraud

2000-01-01

Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type. To determine if this unexpected dichotomy is real or is due to insufficient or biased sampling and to define trends in the evolution of the green algal mitochondrial genome, we sequenced and analyzed the mitochondrial DNA (mtDNA) of Scenedesmus obliquus. This genome is 42,919 bp in size and encodes 42 conserved genes (i.e., large and small subunit rRNA genes, 27 tRNA and 13 respiratory protein-coding genes), four additional free-standing open reading frames with no known homologs, and an intronic reading frame with endonuclease/maturase similarity. No 5S rRNA or ribosomal protein-coding genes have been identified in Scenedesmus mtDNA. The standard protein-coding genes feature a deviant genetic code characterized by the use of UAG (normally a stop codon) to specify leucine, and the unprecedented use of UCA (normally a serine codon) as a signal for termination of translation. The mitochondrial genome of Scenedesmus combines features of both green algal mitochondrial genome types: the presence of a more complex set of protein-coding and tRNA genes is shared with the ancestral type, whereas the lack of 5S rRNA and ribosomal protein-coding genes as well as the presence of fragmented and scrambled rRNA genes are shared with the reduced–derived type of mitochondrial genome organization. Furthermore, the gene content and the fragmentation pattern of the rRNA genes suggest that this genome represents an intermediate stage in the evolutionary process of mitochondrial genome streamlining in green algae. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF204057.] PMID:10854413

Research of epidermal cellular vegetal cycle of intravascular low level laser irradiation in treatment of psoriasis

NASA Astrophysics Data System (ADS)

Zhu, Jing; Bao, Xiaoqing; Zhang, Mei-Jue

2005-07-01

Objective: To research epidermal cellular vegetal cycle and the difference of DNA content between pre and post Intravascular Low Level Laser Irradiation treatment of psoriasis. Method: 15 patients suffered from psoriasis were treated by intravascular low level laser irradiation (output power: 4-5mw, 1 hour per day, a course of treatment is 10 days). We checked the different DNA content of epidermal cell between pre and post treatment of psoriasis and 8 natural human. Then the percentage of each phase among the whole cellular cycle was calculated and the statistical analysis was made. Results: The mean value of G1/S phase is obviously down while G2+M phase increased obviously. T test P<0.05.The related statistical analysis showed significant difference between pre and post treatments. Conclusions: The Intravascular Low Level Laser Irradiation (ILLLI) in treatment of psoriasis is effective according to the research of epidermal cellular vegetal cycle and the difference DNA content of Intravascular Low Level Laser Irradiation between pre and post treatment of psoriasis

Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.

PubMed

Yip, W S Vincent; Shigematsu, Hideki; Taylor, David W; Baserga, Susan J

2016-10-14

Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2'-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Isolation and characterization of ferrous- and sulfur-oxidizing bacteria from Tengchong solfataric region, China.

PubMed

Jiang, Chengying; Liu, Ying; Liu, Yanyang; Guo, Xu; Liu, Shuang-Jiang

2009-01-01

Microbial oxidation and reduction of iron and sulfur are important parts of biogeochemical cycles in acidic environments such as geothermal solfataric regions. Species of Acidithiobacillus and Leptospirillum are the common ferrous-iron and sulfur oxidizers from such environments. This study focused on the Tengchong sofataric region, located in Yunnan Province, Southwest China. Based on cultivation, 9 strains that grow on ferrous-iron and sulfuric compounds were obtained. Analysis of 16S rRNA genes of the 9 strains indicated that they were affiliated to Acidithiobacillus, Alicyclobacillus, Sulfobacillus, Leptospirillum and Acidiphilium. Physiological and phylogenetic studies indicated that two strains (TC-34 and TC-71) might represent two novel members of Alicyclobacillus. Strain TC-34 and TC-71 showed 94.8%-97.1% 16S rRNA gene identities to other species of Alicyclobacillus. Different from the previously described Alicyclobacillus species, strains TC-34 and TC-71 were mesophilic and their cellular fatty acids do not contain omega-cyclic fatty acids. Strain TC-71 was obligately dependent on ferrous-iron for growth. It was concluded that the ferrous-iron oxidizers were diversified and Alicyclobacillus species were proposed to take part in biochemical geocycling of iron in the Tengchong solfataric region.

Roles of the nucleolus in the CAG RNA-mediated toxicity.

PubMed

Tsoi, Ho; Chan, Ho Yin Edwin

2014-06-01

The nucleolus is a subnuclear compartment within the cell nucleus that serves as the site for ribosomal RNA (rRNA) transcription and the assembly of ribosome subunits. Apart from its classical role in ribosomal biogenesis, a number of cellular regulatory roles have recently been assigned to the nucleolus, including governing the induction of apoptosis. "Nucleolar stress" is a term that is used to describe a signaling pathway through which the nucleolus communicates with other subcellular compartments, including the mitochondria, to induce apoptosis. It is an effective mechanism for eliminating cells that are incapable of performing protein synthesis efficiently due to ribosome biogenesis defects. The down-regulation of rRNA transcription is a common cause of nucleolar function disruption that subsequently triggers nucleolar stress, and has been associated with the pathogenesis of neurological disorders such as spinocerebellar ataxias (SCAs) and Huntington's diseases (HD). This article discusses recent advances in mechanistic studies of how expanded CAG trinucleotide repeat RNA transcripts trigger nucleolar stress in SCAs, HD and other trinucleotide repeat disorders. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease. Copyright © 2013 Elsevier B.V. All rights reserved.

A synthetic promoter library for constitutive gene expression in Lactobacillus plantarum.

PubMed

Rud, Ida; Jensen, Peter Ruhdal; Naterstad, Kristine; Axelsson, Lars

2006-04-01

A synthetic promoter library (SPL) for Lactobacillus plantarum has been developed, which generalizes the approach for obtaining synthetic promoters. The consensus sequence, derived from rRNA promoters extracted from the L. plantarum WCFS1 genome, was kept constant, and the non-consensus sequences were randomized. Construction of the SPL was performed in a vector (pSIP409) previously developed for high-level, inducible gene expression in L. plantarum and Lactobacillus sakei. A wide range of promoter strengths was obtained with the approach, covering 3-4 logs of expression levels in small increments of activity. The SPL was evaluated for the ability to drive beta-glucuronidase (GusA) and aminopeptidase N (PepN) expression. Protein production from the synthetic promoters was constitutive, and the most potent promoters gave high protein production with levels comparable to those of native rRNA promoters, and production of PepN protein corresponding to approximately 10-15 % of the total cellular protein. High correlation was obtained between the activities of promoters when tested in L. sakei and L. plantarum, which indicates the potential of the SPL for other Lactobacillus species. The SPL enables fine-tuning of stable gene expression for various applications in L. plantarum.

Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens.

PubMed

Jiao, Yin Shan; Yan, Hui; Ji, Zhao Jun; Liu, Yuan Hui; Sui, Xin Hua; Zhang, Xiao Xia; Wang, En Tao; Chen, Wen Xin; Chen, Wen Feng

2015-02-01

Two novel Gram-stain-negative strains (CCBAU 03422(T) and CCBAU 03415) isolated from root nodules of Sophora flavescens were classified phylogenetically into the genus Phyllobacterium based on the comparative analysis of 16S rRNA and atpD genes. They showed 99.8 % rRNA gene sequence similarities to Phyllobacterium brassicacearum LMG 22836(T), and strain CCBAU 03422(T) showed 91.2 and 88.6 % atpD gene sequence similarities to strains Phyllobacterium endophyticum LMG 26470(T) and Phyllobacterium brassicacearum LMG 22836(T), respectively. Strain CCBAU 03422(T) contained Q-10 as its major quinone and showed a cellular fatty acid profile, carbon source utilization and other phenotypic characteristics differing from type strains of related species. DNA-DNA relatedness (lower than 48.8 %) further confirmed the differences between the novel strains and the type strains of related species. Strain CCBAU 03422(T) could nodulate and fix nitrogen effectively on its original host plant, Sophora flavescens. Based upon the results mentioned above, a novel species named Phyllobacterium sophorae is proposed and the type strain is CCBAU 03422(T) ( = A-6-3(T) = LMG 27899(T) = HAMBI 3508(T)). © 2015 IUMS.

Streptococcus caprae sp. nov., isolated from Iberian ibex (Capra pyrenaica hispanica).

PubMed

Vela, A I; Mentaberre, G; Lavín, S; Domínguez, L; Fernández-Garayzábal, J F

2016-01-01

Biochemical and molecular genetic studies were performed on a novel Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from tonsil samples of two Iberian ibexes. The micro-organism was identified as a streptococcal species based on its cellular, morphological and biochemical characteristics. 16S rRNA gene sequence comparison studies confirmed its identification as a member of the genus Streptococcus, but the organism did not correspond to any species of this genus. The nearest phylogenetic relative of the unknown coccus from ibex was Streptococcus porci 2923-03T (96.6 % 16S rRNA gene sequence similarity). Analysis based on rpoB and sodA gene sequences revealed sequence similarity values lower than 86.0 and 83.8 %, respectively, from the type strains of recognized Streptococcus species. The novel bacterial isolate was distinguished from Streptococcus porci and other Streptococcus species using biochemical tests. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as representing a novel species of the genus Streptococcus, for which the name Streptococcus caprae sp. nov. is proposed. The type strain is DICM07-02790-1CT ( = CECT 8872T = CCUG 67170T).

Extracellular DNA in single- and multiple-species unsaturated biofilms.

PubMed

Steinberger, R E; Holden, P A

2005-09-01

The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.

Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.

PubMed

Osawa, Ro; Fujisawa, Tomohiko; Pukall, Rüdiger

2006-07-01

A Gram-positive, rod-shaped, non-endospore-forming bacterium, strain ASB1(T), able to degrade tannin, was isolated from faeces of the Japanese large wood mouse, Apodemus speciosus. Comparative analysis of the 16S rRNA gene sequence revealed that the strain could be assigned as a member of the genus Lactobacillus. The nearest phylogenetic neighbours were determined as Lactobacillus animalis DSM 20602(T) (98.9 % 16S rRNA gene sequence similarity) and Lactobacillus murinus ASF 361 (98.9 %). Subsequent polyphasic analysis, including automated ribotyping and DNA-DNA hybridization experiments, confirmed that the isolate represents a novel species, for which the name Lactobacillus apodemi sp. nov. is proposed. The DNA G+C content of the novel strain is 38.5 mol%. The cell-wall peptidoglycan is of type A4alpha L-lys-D-asp. The type strain is ASB1(T) (=DSM 16634(T)=CIP 108913(T)).

Phylogenetic characterization and in situ detection of bacterial communities associated with seahorses (Hippocampus guttulatus) in captivity.

PubMed

Balcázar, José L; Lee, Natuschka M; Pintado, José; Planas, Miquel

2010-03-01

Although there are several studies describing bacteria associated with marine fish, the bacterial composition associated with seahorses has not been extensively investigated since these studies have been restricted to the identification of bacterial pathogens. In this study, the phylogenetic affiliation of seahorse-associated bacteria was assessed by 16S rRNA gene sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rRNA analysis. Both methods revealed that Vibrionaceae was the dominant population in Artemia sp. (live prey) and intestinal content of the seahorses, while Rhodobacteraceae was dominant in water samples from the aquaculture system and cutaneous mucus of the seahorses. To our knowledge, this is the first time that bacterial communities associated with healthy seahorses in captivity have been described. Crown Copyright 2010. Published by Elsevier GmbH. All rights reserved.

The laforin-malin complex negatively regulates glycogen synthesis by modulating cellular glucose uptake via glucose transporters.

PubMed

Singh, Pankaj Kumar; Singh, Sweta; Ganesh, Subramaniam

2012-02-01

Lafora disease (LD), an inherited and fatal neurodegenerative disorder, is characterized by increased cellular glycogen content and the formation of abnormally branched glycogen inclusions, called Lafora bodies, in the affected tissues, including neurons. Therefore, laforin phosphatase and malin ubiquitin E3 ligase, the two proteins that are defective in LD, are thought to regulate glycogen synthesis through an unknown mechanism, the defects in which are likely to underlie some of the symptoms of LD. We show here that laforin's subcellular localization is dependent on the cellular glycogen content and that the stability of laforin is determined by the cellular ATP level, the activity of 5'-AMP-activated protein kinase, and the affinity of malin toward laforin. By using cell and animal models, we further show that the laforin-malin complex regulates cellular glucose uptake by modulating the subcellular localization of glucose transporters; loss of malin or laforin resulted in an increased abundance of glucose transporters in the plasma membrane and therefore excessive glucose uptake. Loss of laforin or malin, however, did not affect glycogen catabolism. Thus, the excessive cellular glucose level appears to be the primary trigger for the abnormally higher levels of cellular glycogen seen in LD.

Deciphering Staphylococcus sciuri SAT-17 Mediated Anti-oxidative Defense Mechanisms and Growth Modulations in Salt Stressed Maize (Zea mays L.)

PubMed Central

Akram, Muhammad S.; Shahid, Muhammad; Tariq, Mohsin; Azeem, Muhammad; Javed, Muhammad T.; Saleem, Seemab; Riaz, Saba

2016-01-01

Soil salinity severely affects plant nutrient use efficiency and is a worldwide constraint for sustainable crop production. Plant growth-promoting rhizobacteria, with inherent salinity tolerance, are able to enhance plant growth and productivity by inducing modulations in various metabolic pathways. In the present study, we reported the isolation and characterization of a salt-tolerant rhizobacterium from Kallar grass [Leptochloa fusca (L.) Kunth]. Sequencing of the 16S rRNA gene revealed its lineage to Staphylococcus sciuri and it was named as SAT-17. The strain exhibited substantial potential of phosphate solubilization as well as indole-3-acetic acid production (up to 2 M NaCl) and 1-aminocyclopropane-1-carboxylic acid deaminase activity (up to 1.5 M NaCl). Inoculation of a rifampicin-resistant derivative of the SAT-17 with maize, in the absence of salt stress, induced a significant increase in plant biomass together with decreased reactive oxygen species and increased activity of cellular antioxidant enzymes. The derivative strain also significantly accumulated nutrients in roots and shoots, and enhanced chlorophyll and protein contents in comparison with non-inoculated plants. Similar positive effects were observed in the presence of salt stress, although the effect was more prominent at 75 mM in comparison to higher NaCl level (150 mM). The strain survived in the rhizosphere up to 30 days at an optimal population density (ca. 1 × 106 CFU mL-1). It was concluded that S. sciuri strain SAT-17 alleviated maize plants from salt-induced cellular oxidative damage and enhanced growth. Further field experiments should be conducted, considering SAT-17 as a potential bio-fertilizer, to draw parallels between PGPR inoculation, elemental mobility patterns, crop growth and productivity in salt-stressed semi-arid and arid regions. PMID:27375588

Complete Genome Sequence of Mycobacterium chimaera Strain AH16.

PubMed

Hasan, Nabeeh A; Honda, Jennifer R; Davidson, Rebecca M; Epperson, L Elaine; Bankowski, Matthew J; Chan, Edward D; Strong, Michael

2016-11-23

Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of M. chimaera This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes. Copyright © 2016 Hasan et al.

Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum.

PubMed

Shao, Renfu; Mitani, Harumi; Barker, Stephen C; Takahashi, Mamoru; Fukunaga, Masahito

2005-06-01

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.

Cellular content and biosynthesis of polyamines during rooster spermatogenesis.

PubMed Central

Oliva, R; Vidal, S; Mezquita, C

1982-01-01

The natural polyamines spermine and spermidine, and the diamine putrescine, were extracted from rooster testis cells separated by sedimentation at unit gravity, and from vas-deferens spermatozoa. The ratios spermine/DNA and spermidine/DNA were kept relatively constant throughout spermatogenesis, whereas the ratio putrescine/DNA rose in elongated spermatids. The cellular content of spermine, spermidine and putrescine decreased markedly in mature spermatozoa. Two rate-limiting enzymes in the biosynthetic pathway of polyamines, ornithine decarboxylase and S-adenosyl-L-methionine decarboxylase, showed their highest activities at the end of spermiogenesis and were not detectable in vas-deferens spermatozoa. A marked reduction in cell volume during spermiogenesis without a parallel decrease in the cellular content of polyamines suggests the possibility that the marked changes in chromatin composition and structure occurring in rooster late spermatids could take place in an ambience of high polyamine concentration. Images PLATE 1 PMID:7159401

Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors.

PubMed

Gerasimova, Yulia V; Yakovchuk, Petro; Dedkova, Larisa M; Hecht, Sidney M; Kolpashchikov, Dmitry M

2015-10-01

Mutations in ribosomal RNA (rRNA) have traditionally been detected by the primer extension assay, which is a tedious and multistage procedure. Here, we describe a simple and straightforward fluorescence assay based on binary deoxyribozyme (BiDz) sensors. The assay uses two short DNA oligonucleotides that hybridize specifically to adjacent fragments of rRNA, one of which contains a mutation site. This hybridization results in the formation of a deoxyribozyme catalytic core that produces the fluorescent signal and amplifies it due to multiple rounds of catalytic action. This assay enables us to expedite semi-quantification of mutant rRNA content in cell cultures starting from whole cells, which provides information useful for optimization of culture preparation prior to ribosome isolation. The method requires less than a microliter of a standard Escherichia coli cell culture and decreases analysis time from several days (for primer extension assay) to 1.5 h with hands-on time of ∼10 min. It is sensitive to single-nucleotide mutations. The new assay simplifies the preliminary analysis of RNA samples and cells in molecular biology and cloning experiments and is promising in other applications where fast detection/quantification of specific RNA is required. © 2015 Gerasimova et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Clinorotation influences rDNA and NopA100 localization in nucleoli

NASA Astrophysics Data System (ADS)

Sobol, M. A.; González-Camacho, F.; Rodríguez-Vilariño, V.; Kordyum, E. L.; Medina, F. J.

The nucleolus is the transcription site of rRNA genes as well as the site of processing and initial packaging of their transcripts. The plant nucleolin homologue NopA100 is involved in the regulation of r-chromatin condensation/expansion and rDNA transcription as well as in rRNA processing. We have investigated with immunogold electron microscopy the location of nucleolar DNA and NopA100 in cress root meristematic cells grown under slow horizontal clinorotation, reproducing an important feature of microgravity, namely the absence of an orienting action of a gravity vector, compared to control conditions. We demonstrate redistribution of both rDNA and NopA100 in nucleolar subcomponents induced by clinorotation. Ribosomal DNA concentrated predominantly in fibrillar centers in the form of condensed r-chromatin inclusions and internal non condensed fibrils, redistributing from the dense fibrillar component and the transition zone between fibrillar centers and the dense fibrillar component, recognized as the loci of rDNA transcription. The content of NopA100 was much higher in the inner space of fibrillar centers and reduced in the dense fibrillar component as compared to the control. Based on these data, an effect of slow horizontal clinorotation in lowering the level of rDNA transcription as well as rRNA processing is suggested.

Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function

PubMed Central

He, Yue; Yam, Candice; Pomraning, Kyle; Chin, Jacqueline S. R.; Yew, Joanne Y.; Freitag, Michael; Oliferenko, Snezhana

2014-01-01

Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway. PMID:25318672

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area.

PubMed

Wang, Juanjuan; Sickinger, Maren; Ciobota, Valerian; Herrmann, Martina; Rasch, Helfried; Rösch, Petra; Popp, Jürgen; Küsel, Kirsten

2014-10-15

Iron rich deposits cause clogging the pumps and pipes of dewatering wells in open-cast mines, interfering with their function; however, little is known about either the microbial community structure or their potential role in the formation of these deposits. The microbial diversity and abundance of iron-oxidizing and -reducing bacteria were compared in pipe deposit samples with different levels of encrustation from 16 wells at three lignite mining sites. The groundwater varied in pH values from slightly acidic (4.5) to neutral (7.3), Fe(II) concentrations from 0.48 to 7.55 mM, oxygen content from 1.8 to 5.8 mg L(-1), and dissolved organic carbon (DOC) from 1.43 to 12.59 mg L(-1). There were high numbers of bacterial 16S rRNA gene copies in deposits, up to 2.5 × 10(10) copies g(-1) wet weight. Pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the most abundant phylum (63.3% of the total reads on average), followed by Actinobacteria (10.2%) and Chloroflexi (6.4%). Gallionella-related sequences dominated the bacterial community of pipe deposits and accounted for 48% of total sequence reads. Pipe deposits with amorphous ferrihydrite and schwertmannite mostly contained Gallionella (up to 1.51 × 10(10) 16S rRNA gene copies g(-1) wet weight), while more crystalline deposits showed a higher bacterial diversity. Surprisingly, the abundance of Gallionella was not correlated with groundwater pH, oxygen, or DOC content. Sideroxydans-related 16S rRNA gene copy numbers were one order of magnitude less than Gallionella, followed by acidophilic Ferrovum-related groups. Iron reducing bacteria were detected at rather low abundance, as was expected given the low iron reduction potential, although they could be stimulated by lactate amendment. The overall high abundance of Gallionella suggests that microbes may make major contributions to pipe deposit formation irrespective of the water geochemistry. Their iron oxidation activity might initiate the formation of amorphous iron oxides, potentially providing niches for other microorganisms later after crystallization, and leading to higher bacterial diversity along with deposit accumulation in later stages of clogging. Copyright © 2014 Elsevier Ltd. All rights reserved.

Information content and cross-talk in biological signal transduction: An information theory study

NASA Astrophysics Data System (ADS)

Prasad, Ashok; Lyons, Samanthe

2014-03-01

Biological cells respond to chemical cues provided by extra-cellular chemical signals, but many of these chemical signals and the pathways they activate interfere and overlap with one another. How well cells can distinguish between interfering extra-cellular signals is thus an important question in cellular signal transduction. Here we use information theory with stochastic simulations of networks to address the question of what happens to total information content when signals interfere. We find that both total information transmitted by the biological pathway, as well as its theoretical capacity to discriminate between overlapping signals, are relatively insensitive to cross-talk between the extracellular signals, until significantly high levels of cross-talk have been reached. This robustness of information content against cross-talk requires that the average amplitude of the signals are large. We predict that smaller systems, as exemplified by simple phosphorylation relays (two-component systems) in bacteria, should be significantly much less robust against cross-talk. Our results suggest that mammalian signal transduction can tolerate a high amount of cross-talk without degrading information content, while smaller bacterial systems cannot.

Examination of laser microbeam cell lysis in a PDMS microfluidic channel using time-resolved imaging

PubMed Central

Quinto-Su, Pedro A.; Lai, Hsuan-Hong; Yoon, Helen H.; Sims, Christopher E.; Allbritton, Nancy L.; Venugopalan, Vasan

2008-01-01

We use time-resolved imaging to examine the lysis dynamics of non-adherent BAF-3 cells within a microfluidic channel produced by the delivery of single highly-focused 540 ps duration laser pulses at λ = 532 nm. Time-resolved bright-field images reveal that the delivery of the pulsed laser microbeam results in the formation of a laser-induced plasma followed by shock wave emission and cavitation bubble formation. The confinement offered by the microfluidic channel constrains substantially the cavitation bubble expansion and results in significant deformation of the PDMS channel walls. To examine the cell lysis and dispersal of the cellular contents, we acquire time-resolved fluorescence images of the process in which the cells were loaded with a fluorescent dye. These fluorescence images reveal cell lysis to occur on the nanosecond to microsecond time scale by the plasma formation and cavitation bubble dynamics. Moreover, the time-resolved fluorescence images show that while the cellular contents are dispersed by the expansion of the laser-induced cavitation bubble, the flow associated with the bubble collapse subsequently re-localizes the cellular contents to a small region. This capacity of pulsed laser microbeam irradiation to achieve rapid cell lysis in microfluidic channels with minimal dilution of the cellular contents has important implications for their use in lab-on-a-chip applications. PMID:18305858

Impact of uranium (U) on the cellular glutathione pool and resultant consequences for the redox status of U.

PubMed

Viehweger, Katrin; Geipel, Gerhard; Bernhard, Gert

2011-12-01

Uranium (U) as a redox-active heavy metal can cause various redox imbalances in plant cells. Measurements of the cellular glutathione/glutathione disulfide (GSH/GSSG) by HPLC after cellular U contact revealed an interference with this essential redox couple. The GSH content remained unaffected by 10 μM U whereas the GSSG level immediately increased. In contrast, higher U concentrations (50 μM) drastically raised both forms. Using the Nernst equation, it was possible to calculate the half-cell reduction potential of 2GSH/GSSG. In case of lower U contents the cellular redox environment shifted towards more oxidizing conditions whereas the opposite effect was obtained by higher U contents. This indicates that U contact causes a consumption of reduced redox equivalents. Artificial depletion of GSH by chlorodinitrobenzene and measuring the cellular reducing capacity by tetrazolium salt reduction underlined the strong requirement of reduced redox equivalents. An additional element of cellular U detoxification mechanisms is the complex formation between the heavy metal and carboxylic functionalities of GSH. Because two GSH molecules catalyze electron transfers each with one electron forming a dimer (GSSG) two UO(2) (2+) are reduced to each UO(2) (+) by unbound redox sensitive sulfhydryl moieties. UO(2) (+) subsequently disproportionates to UO(2) (2+) and U(4+). This explains that in vitro experiments revealed a reduction to U(IV) of only around 33% of initial U(VI). Cellular U(IV) was transiently detected with the highest level after 2 h of U contact. Hence, it can be proposed that these reducing processes are an important element of defense reactions induced by this heavy metal.

New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria.

PubMed

Zhou, Zhichao; Chen, Jing; Meng, Han; Dvornyk, Volodymyr; Gu, Ji-Dong

2017-02-01

PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH 4 + and NH 4 + /Σ(NO 3 - + NO 2 - ) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.

The association of TIF-IA and polymerase I mediates promoter recruitment and regulation of ribosomal RNA transcription in Acanthamoeba castellanii.

PubMed

Gogain, Joseph C; Paule, Marvin R

2005-01-01

Large amounts of energy are expended for the construction of the ribosome during both transcription and processing, so it is of utmost importance for the cell to efficiently regulate ribosome production. Understanding how this regulation occurs will provide important insights into cellular growth control and into the coordination of gene expression mediated by all three transcription systems. Ribosomal RNA (rRNA) transcription rates closely parallel the need for protein synthesis; as a cell approaches stationary phase or encounters conditions that negatively affect either growth rate or protein synthesis, rRNA transcription is decreased. In eukaryotes, the interaction of RNA polymerase I (pol I) with the essential transcription initiation factor IA (TIF-IA) has been implicated in this downregulation of transcription. In agreement with the first observation that rRNA transcription is regulated by altering recruitment of pol I to the promoter in Acanthamoeba castellanii, we show here that pol I and an 80-kDa homologue of TIF-IA are found tightly associated in pol I fractions competent for specific transcription. Disruption of the pol I-TIF-IA complex is mediated by a specific dephosphorylation of either pol I or TIF-IA. Phosphatase treatment of TIF-IA-containing A. castellanii pol I fractions results in a downregulation of both transcriptional activity and promoter binding, reminiscent of the inactive pol I fractions purified from encysted cells. The fraction of pol I competent for promoter recruitment is enriched in TIF-IA relative to that not bound by immobilized promoter DNA. This downregulation coincides with an altered electrophoretic mobility of TIF-IA, suggesting at least it is phosphorylated.

Interleukin 6 downregulates p53 expression and activity by stimulating ribosome biogenesis: a new pathway connecting inflammation to cancer

PubMed Central

Brighenti, E; Calabrese, C; Liguori, G; Giannone, F A; Trerè, D; Montanaro, L; Derenzini, M

2014-01-01

Chronic inflammation is an established risk factor for the onset of cancer, and the inflammatory cytokine IL-6 has a role in tumorigenesis by enhancing proliferation and hindering apoptosis. As factors stimulating proliferation also downregulate p53 expression by enhancing ribosome biogenesis, we hypothesized that IL-6 may cause similar changes in inflamed tissues, thus activating a mechanism that favors neoplastic transformation. Here, we showed that IL-6 downregulated the expression and activity of p53 in transformed and untransformed human cell lines. This was the consequence of IL-6-dependent stimulation of c-MYC mRNA translation, which was responsible for the upregulation of rRNA transcription. The enhanced rRNA transcription stimulated the MDM2-mediated proteasomal degradation of p53, by reducing the availability of ribosome proteins for MDM2 binding. The p53 downregulation induced the acquisition of cellular phenotypic changes characteristic of epithelial–mesenchymal transition, such as a reduced level of E-cadherin expression, increased cell invasiveness and a decreased response to cytotoxic stresses. We found that these changes also occurred in colon epithelial cells of patients with ulcerative colitis, a very representative example of chronic inflammation at high risk for tumor development. Histochemical and immunohistochemical analysis of colon biopsy samples showed an upregulation of ribosome biogenesis, a reduced expression of p53, together with a focal reduction or absence of E-cadherin expression in chronic colitis in comparison with normal mucosa samples. These changes disappeared after treatment with anti-inflammatory drugs. Taken together, the present results highlight a new mechanism that may link chronic inflammation to cancer, based on p53 downregulation, which is activated by the enhancement of rRNA transcription upon IL-6 exposure. PMID:24531714

[Community structure and phylogenetic analysis of cyanobacteria in cryoconite from surface of the Glacier No. 1 in the Tianshan Mountains].

PubMed

Ni, Xuejiao; Qi, Xing'e; Gu, Yanling; Zheng, Xiaoji; Dong, Juan; Ni, Yongqing; Cheng, Guodong

2014-11-04

The purpose of this study is to characterize the community composition and phylogenetic analysis of cyanobacteria from supraglacial cryoconite of the Glacier No. 1 in the Tianshan Mountains, China. We amplified 16S rRNA genes from the extracted cryoconite DNA by PCR with 2 pairs of cyanobacteria-specific primers. Amplificon was used to construct 16S rRNA genes clone library. The estimation of species richness, diversity indices, and rarefaction curve of the 16S rRNA genes library were determined based on representative phylotypes (OTUs). Analysis of 16S rRNA gene sequences allowed grouping of 101 clones into 12 phylotypes (OTUs) using a cut-off of 97% identity. The phylogenetic analysis revealed that most of sequences affiliated to the order Oscillatoriales and Chroococcales except that three were unclassified. The clone library was dominated by representatives of the order Oscillatoriales (81% of the total clones), and the most abundant organisms within this order were in the genus Phormidium (68 clones) including clones grouping into four phylotypes. The only clone of Chroococcales was closely related to the genus Chamaesiphon with 97% similarity. In addition, comparison of soil chemical properties between different habitats indicated that supraglacial cryoconite supported significantly higher the content of available phosphorus and potassium, nitrate nitrogen and organic matter compared with the forefield of the Glacier No. 1. The diversity index of cyanobacteria were relatively high in supraglacial cryoconite of the Glacier No. 1 in the Tianshan Mountains. The community structure was dominated by members of the genus Phormidium. This study may enrich our knowledge on biogeochemical processes and ecological distribution of cyanobacterial populations in glacial ecosystem.

Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea.

PubMed

Swan, Brandon K; Ehrhardt, Christopher J; Reifel, Kristen M; Moreno, Lilliana I; Valentine, David L

2010-02-01

Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, and Crenarchaeota. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA. Archaea were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of Bacteria. The relative abundance of Crenarchaeota was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of Euryarchaeota and Crenarchaeota, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% [wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.

Complete mitochondrial genome of the agarophyte red alga Gelidium vagum (Gelidiales).

PubMed

Yang, Eun Chan; Kim, Kyeong Mi; Boo, Ga Hun; Lee, Jung-Hyun; Boo, Sung Min; Yoon, Hwan Su

2014-08-01

We describe the first complete mitochondrial genome of Gelidium vagum (Gelidiales) (24,901 bp, 30.4% GC content), an agar-producing red alga. The circular mitochondrial genome contains 43 genes, including 23 protein-coding, 18 tRNA and 2 rRNA genes. All the protein-coding genes have a typical ATG start codon. No introns were found. Two genes, secY and rps12, were overlapped by 41 bp.

Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom.

PubMed

Tiwari, Sandeep; Jamal, Syed Babar; Oliveira, Leticia Castro; Clermont, Dominique; Bizet, Chantal; Mariano, Diego; de Carvalho, Paulo Vinicius Sanches Daltro; Souza, Flavia; Pereira, Felipe Luiz; de Castro Soares, Siomar; Guimarães, Luis C; Dorella, Fernanda; Carvalho, Alex; Leal, Carlos; Barh, Debmalya; Figueiredo, Henrique; Hassan, Syed Shah; Azevedo, Vasco; Silva, Artur

2016-08-11

In this work, we describe a set of features of Corynebacterium auriscanis CIP 106629 and details of the draft genome sequence and annotation. The genome comprises a 2.5-Mbp-long single circular genome with 1,797 protein-coding genes, 5 rRNA, 50 tRNA, and 403 pseudogenes, with a G+C content of 58.50%. Copyright © 2016 Tiwari et al.

The Role of Tetraether Lipid Composition in the Adaptation of Thermophilic Archaea to Acidity

PubMed Central

Boyd, Eric S.; Hamilton, Trinity L.; Wang, Jinxiang; He, Liu; Zhang, Chuanlun L.

2013-01-01

Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively) lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings), the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly correlated with the similarity in the composition of C- and P-iGDGT lipids. Taken together, these data suggest that the ability to adjust the composition of GDGT lipid membranes played a central role in the diversification of archaea into or out of environments characterized by extremes of low pH and high temperature. PMID:23565112

Geomicrobial characterization of a 60 m long permafrost core from Svalbard

NASA Astrophysics Data System (ADS)

Fromreide, Siren; Tore Mørkved, Pål; Gilbert, Graham Lewis; Christiansen, Hanne H.; Reigstad, Laila

2014-05-01

In connection with a planned CO2 storage pilot project in the Arctic, a 60 m long permafrost core was drilled in Adventdalen, Svalbard. The on-shore drilling was performed through mainly marine and deltafront sediments, ending at the bedrock. The core has undergone detailed analyses of sedimentary stratigraphy, age, as well as the permafrost ice and carbon content at The University Centre in Svalbard (UNIS), and at the Center for Permafrost (CENPERM), Copenhagen. The main aim of the study presented here is to link the geochemical properties of the permafrost to the microbial community structure and its potential functions. As little is known about microbial life in permafrost at such depths this study will contribute to the understanding of these inaccessible ecosystems. A baseline geomicrobial description of 7 different depths in the 3 - 60 m interval of the permafrost core was done by culture independent methods such as 16S rRNA amplicon 454 pyrosequencing and functional and ribosomal gene quantifications. Additionally, geochemical analyses of the extracted pore water have been performed, as well as measurements of carbon content and major elements. The enumeration of the total prokaryotic community indicated similar numbers of bacteria and archaea down to approximately 50 m depth, while below this depth there was a dominance of archaeal cells. The bacterial 16S rRNA copy numbers ranged between 108 copies per gram sediment at 3 m depth to 104 copies per gram at the bedrock. Concerning the archaeal cells, the 16S rRNA copy numbers per gram sediment were in the range of 107 at the top of the core, ending at 105in the top of the bedrock. Detection and quantification of selected functional marker genes indicated high numbers of sulphate reducing bacteria at certain sediment depths, and a significant potential for microbial methanogenic activity throughout the core. Correlations studies between geochemical data and microbial community composition are currently ongoing.

Abiotic and biotic factors responsible for antimonite oxidation in Agrobacterium tumefaciens GW4

PubMed Central

Li, Jingxin; Yang, Birong; Shi, Manman; Yuan, Kai; Guo, Wei; Wang, Qian; Wang, Gejiao

2017-01-01

Antimonite [Sb(III)]-oxidizing bacteria can transform the toxic Sb(III) into the less toxic antimonate [Sb(V)]. Recently, the cytoplasmic Sb(III)-oxidase AnoA and the periplasmic arsenite [As(III)] oxidase AioAB were shown to responsible for bacterial Sb(III) oxidation, however, disruption of each gene only partially decreased Sb(III) oxidation efficiency. This study showed that in Agrobacterium tumefaciens GW4, Sb(III) induced cellular H2O2 content and H2O2 degradation gene katA. Gene knock-out/complementation of katA, anoA, aioA and anoA/aioA and Sb(III) oxidation and growth experiments showed that katA, anoA and aioA were essential for Sb(III) oxidation and resistance and katA was also essential for H2O2 resistance. Furthermore, linear correlations were observed between cellular H2O2 and Sb(V) content in vivo and chemical H2O2 and Sb(V) content in vitro (R2 = 0.93 and 0.94, respectively). These results indicate that besides the biotic factors, the cellular H2O2 induced by Sb(III) also catalyzes bacterial Sb(III) oxidation as an abiotic oxidant. The data reveal a novel mechanism that bacterial Sb(III) oxidation is associated with abiotic (cellular H2O2) and biotic (AnoA and AioAB) factors and Sb(III) oxidation process consumes cellular H2O2 which contributes to microbial detoxification of both Sb(III) and cellular H2O2. PMID:28252030

Abiotic and biotic factors responsible for antimonite oxidation in Agrobacterium tumefaciens GW4

NASA Astrophysics Data System (ADS)

Li, Jingxin; Yang, Birong; Shi, Manman; Yuan, Kai; Guo, Wei; Wang, Qian; Wang, Gejiao

2017-03-01

Antimonite [Sb(III)]-oxidizing bacteria can transform the toxic Sb(III) into the less toxic antimonate [Sb(V)]. Recently, the cytoplasmic Sb(III)-oxidase AnoA and the periplasmic arsenite [As(III)] oxidase AioAB were shown to responsible for bacterial Sb(III) oxidation, however, disruption of each gene only partially decreased Sb(III) oxidation efficiency. This study showed that in Agrobacterium tumefaciens GW4, Sb(III) induced cellular H2O2 content and H2O2 degradation gene katA. Gene knock-out/complementation of katA, anoA, aioA and anoA/aioA and Sb(III) oxidation and growth experiments showed that katA, anoA and aioA were essential for Sb(III) oxidation and resistance and katA was also essential for H2O2 resistance. Furthermore, linear correlations were observed between cellular H2O2 and Sb(V) content in vivo and chemical H2O2 and Sb(V) content in vitro (R2 = 0.93 and 0.94, respectively). These results indicate that besides the biotic factors, the cellular H2O2 induced by Sb(III) also catalyzes bacterial Sb(III) oxidation as an abiotic oxidant. The data reveal a novel mechanism that bacterial Sb(III) oxidation is associated with abiotic (cellular H2O2) and biotic (AnoA and AioAB) factors and Sb(III) oxidation process consumes cellular H2O2 which contributes to microbial detoxification of both Sb(III) and cellular H2O2.

Computer vision in cell biology.

PubMed

Danuser, Gaudenz

2011-11-23

Computer vision refers to the theory and implementation of artificial systems that extract information from images to understand their content. Although computers are widely used by cell biologists for visualization and measurement, interpretation of image content, i.e., the selection of events worth observing and the definition of what they mean in terms of cellular mechanisms, is mostly left to human intuition. This Essay attempts to outline roles computer vision may play and should play in image-based studies of cellular life. Copyright © 2011 Elsevier Inc. All rights reserved.

RF Microalgal lipid content characterization

PubMed Central

Ahmad, Mahmoud Al; Al-Zuhair, Sulaiman; Taher, Hanifa; Hilal-Alnaqbi, Ali

2014-01-01

Most conventional techniques for the determination of microalgae lipid content are time consuming and in most cases are indirect and require excessive sample preparations. This work presents a new technique that utilizes radio frequency (RF) for rapid lipid quantification, without the need for sample preparation. Tests showed that a shift in the resonance frequency of a RF open-ended coaxial resonator and a gradual increase in its resonance magnitude may occur as the lipids content of microalgae cells increases. These response parameters can be then calibrated against actual cellular lipid contents and used for rapid determination of the cellular lipids. The average duration of lipid quantification using the proposed technique was of about 1 minute, which is significantly less than all other conventional techniques, and was achieved without the need for any time consuming treatment steps. PMID:24870372

Advances in Predictive Toxicology for Discovery Safety through High Content Screening.

PubMed

Persson, Mikael; Hornberg, Jorrit J

2016-12-19

High content screening enables parallel acquisition of multiple molecular and cellular readouts. In particular the predictive toxicology field has progressed from the advances in high content screening, as more refined end points that report on cellular health can be studied in combination, at the single cell level, and in relatively high throughput. Here, we discuss how high content screening has become an essential tool for Discovery Safety, the discipline that integrates safety and toxicology in the drug discovery process to identify and mitigate safety concerns with the aim to design drug candidates with a superior safety profile. In addition to customized mechanistic assays to evaluate target safety, routine screening assays can be applied to identify risk factors for frequently occurring organ toxicities. We discuss the current state of high content screening assays for hepatotoxicity, cardiotoxicity, neurotoxicity, nephrotoxicity, and genotoxicity, including recent developments and current advances.

Analysis of Cellular DNA Content by Flow Cytometry.

PubMed

Darzynkiewicz, Zbigniew; Huang, Xuan; Zhao, Hong

2017-10-02

Cellular DNA content can be measured by flow cytometry with the aim of : (1) revealing cell distribution within the major phases of the cell cycle, (2) estimating frequency of apoptotic cells with fractional DNA content, and/or (3) disclosing DNA ploidy of the measured cell population. In this unit, simple and universally applicable methods for staining fixed cells are presented, as are methods that utilize detergents and/or proteolytic treatment to permeabilize cells and make DNA accessible to fluorochrome. Additionally, supravital cell staining with Hoechst 33342, which is primarily used for sorting live cells based on DNA-content differences for their subsequent culturing, is described. Also presented are methods for staining cell nuclei isolated from paraffin-embedded tissues. Available algorithms are listed for deconvolution of DNA-content-frequency histograms to estimate percentage of cells in major phases of the cell cycle and frequency of apoptotic cells with fractional DNA content. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley and Sons, Inc.

Analysis of Cellular DNA Content by Flow Cytometry.

PubMed

Darzynkiewicz, Zbigniew; Huang, Xuan; Zhao, Hong

2017-11-01

Cellular DNA content can be measured by flow cytometry with the aim of : (1) revealing cell distribution within the major phases of the cell cycle, (2) estimating frequency of apoptotic cells with fractional DNA content, and/or (3) disclosing DNA ploidy of the measured cell population. In this unit, simple and universally applicable methods for staining fixed cells are presented, as are methods that utilize detergents and/or proteolytic treatment to permeabilize cells and make DNA accessible to fluorochrome. Additionally, supravital cell staining with Hoechst 33342, which is primarily used for sorting live cells based on DNA-content differences for their subsequent culturing, is described. Also presented are methods for staining cell nuclei isolated from paraffin-embedded tissues. Available algorithms are listed for deconvolution of DNA-content-frequency histograms to estimate percentage of cells in major phases of the cell cycle and frequency of apoptotic cells with fractional DNA content. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley and Sons, Inc.

Contribution of high-content imaging technologies to the development of anti-infective drugs.

PubMed

Ang, Michelle Lay Teng; Pethe, Kevin

2016-08-01

Originally developed to study fundamental aspects of cellular biology, high-content imaging (HCI) was rapidly adapted to study host-pathogen interactions at the cellular level and adopted as a technology of choice to unravel disease biology. HCI platforms allow for the visualization and quantification of discrete phenotypes that cannot be captured using classical screening approaches. A key advantage of high-content screening technologies lies in the possibility to develop and interrogate physiologically significant, predictive ex vivo disease models that reproduce complex conditions relevant for infection. Here we review and discuss recent advances in HCI technologies and chemical biology approaches that are contributing to an increased understanding of the intricate host-pathogen interrelationship on the cellular level, and which will foster the development of novel therapeutic approaches for the treatment of human bacterial and protozoan infections. © 2016 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of ISAC. © 2016 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of ISAC.

Propioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying.

PubMed

Zhang, Lei; Li, Qiqi; Chen, Chaoqiong; Li, Xin; Li, Muhang; Hu, Jingjiang; Shen, Xihui

2017-10-01

A Gram-reaction-positive, facultatively anaerobic, rod-shaped and non-motile bacterial strain, designated TEYR-7 T , was isolated from the leaves of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, northwest China. Growth of strain TEYR-7 T occurred at 15-37 °C (optimum, 28-30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0-1 %). Propionate and acetate were produced from glucose fermentation. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TEYR-7 T was a member of the phylum Actinobacteria, exhibiting the highest sequence similarity to Propioniciclava tarda DSM 22130 T (94.3 %). The only respiratory quinone detected in strain TEYR-7 T was menaquinone MK-9(H4) and the major cellular fatty acids (>10 %) were anteiso-C15 : 0 and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and three unidentified lipids. The genomic DNA G+C content was 71.2 mol%. meso-Diaminopimelic acid was detected in the peptidoglycan. On the basis of data from the present polyphasic taxonomic study, strain TEYR-7 T is considered to represent a novel species of the genus Propioniciclava, for which the name Propioniciclava sinopodophylli sp. nov. is proposed. The type strain is TEYR-7 T (=CCTCC AB 2015257 T =KCTC 33808 T ).

Blastococcus colisei sp. nov, isolated from an archaeological amphitheatre.

PubMed

Hezbri, Karima; Nouioui, Imen; Rohde, Manfred; Schumann, Peter; Gtari, Maher; Klenk, Hans-Peter; Montero-Calasanz, Maria Del Carmen; Ghodhbane-Gtari, Faten

2017-03-01

The taxonomic position of an actinobacterial isolate, designated strain BMG 822 T , isolated from limestone from the Amphitheater of El Jem (Coliseum Thysdrus), Tunisia, was established using a polyphasic approach. Strain BMG 822 T was found to grow well at 30 °C and pH 6.5-8.0, and to be coral-coloured, Gram-positive, catalase and oxidase negative. Whole cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, glucose, galactose and ribose. The phospholipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified glycophospholipid and six unidentified phospholipids. MK-9(H 4 ) was found to be the predominant menaquinone, followed by MK-9(H 2 ) and MK-9. The major cellular fatty acids were identified as iso-C 16:0 , C 18:1 ω9c, C 17:1 ω8c and iso-H-C 16:1 . The G+C content of the DNA (73.2%) is typical of the genus. High degrees of 16S rRNA gene sequence similarity were found with the type strains of the genus Blastococcus (97.1-98.3%) followed by the type strains of Modestobacter (96.8-97.8%). Based on the above data and the phenotypic differences from the type strains of Blastococcus species, it is proposed that the isolate BMG 822 T (=DSM 46837 T =CECT 8823 T ) should be classified as the type strain of a novel species, Blastococcus colisei sp. nov.

Flavobacterium kingsejongi sp. nov., a carotenoid-producing species isolated from Antarctic penguin faeces.

PubMed

Choi, Jun Young; Kim, Jin Ho; Lee, Pyung Cheon

2018-03-01

Taxonomic studies were carried out on a carotenoid-producing strain, designated WV39 T , isolated from the faeces of Antarctic penguins. Cells of strain WV39 T were Gram-stain-negative, strictly aerobic, yellow and rod-shaped. 16S rRNA gene sequence analysis revealed that strain WV39 T was closely related to Flavobacterium qiangtangense JCM 19739 T (96.3 % similarity), Flavobacterium noncentrifugens NBRC 108844 T (95.5 %) and Flavobacterium aquatile LMG 4008 T (94.9 %). The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-6 was the sole quinone identified, and the major pigment was zeaxanthin. The major polar lipid was phosphatidylethanolamine. DNA-DNA relatedness of strain WV39 T with respect to its closest phylogenetic neighbours was 41.8 % for F. qiangtangense JCM 19739 T , 25.5 % for F. aquatile LMG 4008 T and 25.2 % for F. noncentrifugens NBRC 108844 T . The DNA G+C content of strain WV39 T was 39.8 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain WV39 T is concluded to represent a novel species of the genus Flavobacterium, for which the name Flavobacteriumkingsejongi sp. nov. is proposed. The type strain is WV39 T (=KCTC 42908 T =CECT 9085 T ).

Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand.

PubMed

Chamroensaksri, Nitcha; Tanasupawat, Somboon; Akaracharanya, Ancharida; Visessanguan, Wonnop; Kudo, Takuji; Itoh, Takashi

2009-04-01

A Gram-negative, facultatively anaerobic, moderately halophilic bacterium, strain ND1-1(T), was isolated from fermented fish (pla-ra) in Thailand. The cells were curved rods, motile and non-endospore-forming. The novel strain grew optimally at 37 degrees C, at pH 8 and in the presence of 9-10 % (w/v) NaCl. The predominant respiratory lipoquinone was Q-8. The major cellular fatty acids were C(16 : 0) and C(12 : 0). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 49.0 mol%. Comparative 16S rRNA gene sequence analyses indicated that strain ND1-1(T) was closely related to Salinivibrio costicola, which comprises three subspecies, and Salinivibrio proteolyticus with gene sequence similarities of 98.3-98.6 %. Strain ND1-1(T) showed low levels of DNA-DNA relatedness with S. costicola subsp. costicola JCM 15095(T) (33.2 %), S. costicola subsp. alcaliphilus DSM 16359(T) (38.4 %), S. costicola subsp. vallismortis JCM 15096(T) (59.7 %), and S. proteolyticus AF-2004(T) (42.1 %). On the basis of the physiological and biochemical characteristics and the molecular data presented, strain ND1-1(T) should be classified as a novel species of the genus Salinivibrio for which the name Salinivibrio siamensis sp. nov. is proposed. The type strain is ND1-1(T) (=JCM 14472(T)=PCU 301(T)=TISTR 1810(T)).

Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster.

PubMed

Baek, Chaeyun; Kim, Eunji; Shin, Su-Kyoung; Choi, Sungmi; Yi, Hana

2017-10-01

A Gram-negative, motile, rod-shaped, and aerobic bacterial strain, designated LPB0072 T , was isolated from a Pacific oyster (Crassostrea gigas). Autotrophic growth with hydrogen gas was not observed. Cells oxidized thiosulfate to sulfate and reduced nitrate to nitrite. The complete genome sequence of strain LPB0072 T (CP017476) is 4.94 Mb in length and contains 4459 protein-coding genes, with a G+C content of 61.3 mol%. Analysis of the 16S rRNA gene sequence indicated that strain LPB0072 T belongs to the genus Hydrogenophaga, with greatest sequence similarity to the type strain of Hydrogenophaga taeniospiralis (97.5 %). The isoprenoid quinone (Q-8) and the major cellular fatty acids (C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω6c) identified were concordant with the chemotaxonomic properties of the genus Hydrogenophaga. The average nucleotide identities with closely related species were below the suggested boundary for species delineation, indicating that the isolate is a novel species. Numerous physiological and biochemical features also distinguished the isolate from other known Hydrogenophaga species. Based on the polyphasic data presented in this study, strain LPB0072 T should be classified as a novel species in the genus Hydrogenophaga, and the name Hydrogenophaga crassostreae sp. nov. is proposed. The type strain is LPB0072 T (=KACC 18705 T =JCM 31188 T ).

Bacillus vanillea sp. nov., Isolated from the Cured Vanilla Bean.

PubMed

Chen, Yong-gan; Gu, Feng-lin; Li, Ji-hua; Xu, Fei; He, Shu-zhen; Fang, Yi-ming

2015-02-01

A Gram-positive bacterium, designated strain XY18(T), was isolated from a cured vanilla bean in Hainan province, China. Cells were rod-shaped, endospore producing, and peritrichous flagella. Strain XY18(T) grew at salinities of 0-8 % (w/v) NaCl (optimally 1-4 %), pH 4.0-8.0 (optimally 5.0-7.0 %) and temperature range 20-45 °C (optimally 28-35 °C). The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, and iso-C17:0. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XY18(T) was a member of the genus Bacillus, and closely related to B. amyloliquefaciens NBRC 15535(T) and B. siamensis PD-A10(T), with 99.1 and 99.2 % sequence similarity, respectively. However, the DNA-DNA hybridization value between strain XY18(T) and B. amyloliquefaciens NBRC 15535(T) was 35.7 %. The genomic DNA G+C content of strain XY18(T) was 46.4 mol%, significantly differed from B. siamensis PD-A10(T) (41.4 %), which was higher than the range of 4 % indicative of species. On the basis of polyphasic taxonomic study, including phenotypic features, chemotaxonomy, and phylogenetic analyses, strain XY18(T) represents a novel species within the genus Bacillus, for which the name Bacillus vanillea sp. nov. is proposed. The type strain is XY18(T) (=CGMCC 8629 = NCCB 100507).

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies.

PubMed

Roller, Benjamin R K; Stoddard, Steven F; Schmidt, Thomas M

2016-09-12

The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce and when they are abundant 1,2 , but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here, we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction-growth rate and growth efficiency-which are favoured under contrasting regimes of resource availability 3,4 . We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, and the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings imply that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements 5 or inferences 6,7 .

Halomonas sinaiensis sp. nov., a novel halophilic bacterium isolated from a salt lake inside Ras Muhammad Park, Egypt.

PubMed

Romano, Ida; Lama, Licia; Orlando, Pierangelo; Nicolaus, Barbara; Giordano, Assunta; Gambacorta, Agata

2007-11-01

An alkalitolerant and halotolerant bacterium, designated strain Sharm was isolated from a salt lake inside Ras Muhammad. The morphological, physiological and genetic characteristics were compared with those of related species of the genus Halomonas. The isolate grew optimally at pH 7.0, 5-15% NaCl at 35 degrees C. The cells were Gram-negative rods, facultative anaerobes. They accumulated glycine-betaine, as a major osmolyte, and ectoine and glutamate as minor components. The strain Sharm(T) biosynthetised alpha-glucosidase. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and a novel phosphoglycolipid as major components. Ubiquinone with nine repetitive unities (Q9) was the only quinone found and, nC16:0 and C19:0 with cyclopropane were the main cellular fatty acids, accounting for 87.3% of total fatty acids. The G + C content of the genomic DNA was 64.7 mol %. The 16S rRNA sequence analysis indicated that strain Sharm was a member of the genus Halomonas. The closest relatives of the strain Sharm were Halomonas elongata and Halomonas eurihalina. However, DNA-DNA hybridisation results clearly indicated that strain Sham was a distinct species of Halomonas. On the basis of the evidence, we propose to assign strain Sharm as a new species of the genus Halomonas, H. sinaiensis sp. nov, with strain Sharm(T) as the type strain (DSM 18067(T); ATCC BAA-1308(T)).

Nesterenkonia pannonica sp. nov., a novel alkaliphilic and moderately halophilic actinobacterium.

PubMed

Borsodi, Andrea K; Szili-Kovács, Tibor; Schumann, Peter; Spröer, Cathrin; Márialigeti, Károly; Tóth, Erika

2017-10-01

An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35 T , was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35 T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35 T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3 T (97.9 %). The DNA-DNA relatedness between BV-35 T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35 T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35 T (=DSM 29786 T =NCAIM B 02606 T ).

Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov.

PubMed

Du, Zong-Jun; Wang, Ying; Dunlap, Christopher; Rooney, Alejandro P; Chen, Guan-Jun

2014-05-01

The taxonomic characteristics of two bacterial strains, FH5T and SS4, isolated from enrichment cultures obtained from two distinct marine environments, were determined. These bacteria were Gram-stain-negative, facultatively anaerobic rods. Growth occurred at 20-40 °C (optimum, 28-32 °C), pH 5.5-9.0 (optimum, pH 7.0-7.5) and in the presence of 1-7% NaCl (optimum, 2-4%). The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. Menaquinone 7 (MK-7) was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, an unkown phospholipid and an unknown lipid. The DNA G+C contents of strains FH5T and SS4 were both determined to be 42.0 mol%. The results of DNA-DNA hybridization studies indicated that the FH5T and SS4 genomes share greater than 95% relatedness. The strains formed a distinct phyletic line within the class Bacteroidia, with less than 89.4% sequence similarity to their closest relatives with validly published names. On the basis of physiological and biochemical characteristics, 16S rRNA gene sequences and chemical properties, a novel genus and species, Draconibacterium orientale gen. nov., sp. nov., within the class Bacteroidia, are proposed, with strain FH5T (=DSM 25947T=CICC 10585T) as the type strain. In addition, a new family, Draconibacteriaceae fam. nov., is proposed to accommodate Draconibacterium gen. nov.

Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium, isolated from rice rhizosphere.

PubMed

Lv, Haoxin; Masuda, Sachiko; Fujitani, Yoshiko; Sahin, Nurettin; Tani, Akio

2017-04-01

A novel facultatively methanol-utilizing bacterial strain, SM30T, was isolated from rice rhizosphere. Strain SM30T was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30T showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30T is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18 : 1ω7c and 18 : 1ω6c) and cyclo 19 : 0ω8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30T represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30T (=NBRC 111955T=DSM 102969T).

Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem.

PubMed

Dedysh, Svetlana N; Didriksen, Alena; Danilova, Olga V; Belova, Svetlana E; Liebner, Susanne; Svenning, Mette M

2015-10-01

An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1–8.0 (optimum pH 5.2–6.5) at temperatures between 6 and 32 °C (optimum 18–25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T).

Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.

PubMed

Woo, Sung-Geun; Srinivasan, Sathiyaraj; Yang, Jihoon; Jung, Yong-An; Kim, Myung Kyum; Lee, Myungjin

2012-05-01

Strain MJ31(T), a gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31(T) belonged to the genus Nocardioides, appearing most closely related to Nocardioides dubius KSL-104(T) (98.6 % sequence similarity), Nocardioides jensenii DSM 20641(T) (97.6 %), Nocardioides daedukensis MDN22(T) (97.2 %) and Nocardioides mesophilus MSL-22(T) (97.0 %). The chemotaxonomic properties of strain MJ31(T) were consistent with those of the genus Nocardioides: MK-8(H(4)) was the predominant menaquinone, iso-C(16 : 0), iso-C(17 : 0) and C(18 : 1)ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on LL-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31(T) was 71.2 mol%. Some differential phenotypic properties and low DNA-DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31(T) represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31(T) ( = KCTC 19772(T) = JCM 16922(T)).

Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field.

PubMed

Tang, Jingwei; Huang, Jing; Qiao, Zixu; Wang, Rui; Wang, Gejiao

2016-10-01

Strain TBZ30T was isolated from soil of a heavy-metal-contaminated paddy field. Cells of strain TBZ30T were Gram-staining-negative, rod-shaped, non-motile and non-spore-forming. The isolate was strictly aerobic, pink-pigmented, catalase- and oxidase-positive and produced exopolysaccharides. On the basis of 16S rRNA gene phylogeny, strain TBZ30T belonged to the genus Mucilaginibacter and appeared most closely related to Mucilaginibacter gynuensis YC7003T (95.8 %), Mucilaginibacter litoreus BR-18T (95.4 %) and Mucilaginibacter mallensis MP1X4T (95.4 %). Strain TBZ30T contained menaquinone-7 as the only ubiquinone. The main cellular fatty acids included summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and C16 : 1ω5c. The polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, four unidentified aminolipids, three unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 49.0 mol%. On the basis of polyphasic taxonomy analyses, strain TBZ30T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter pedocola sp. nov. is proposed. The type strain is TBZ30T (=KCTC 42833T=CCTCC AB 2015301T).

Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer.

PubMed

Urios, Laurent; Intertaglia, Laurent; Magot, Michel

2013-01-01

A Gram-negative bacterium, designated TF5-37.2-LB10(T), was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10(T) contained menaquinone 7 and its major fatty acids were iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c), iso-C(17 : 0) 3-OH and iso-C(17 : 1)ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10(T) within the genus Pedobacter, family Sphingobacteriaceae. Pedobacter composti TR6-06(T) and Pedobacter oryzae DSM 19973(T) were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10(T) (= DSM 23085(T) = CIP 110085(T) = MOLA 820(T)).

Gaetbulicola byunsanensis gen. nov., sp. nov., isolated from tidal flat sediment.

PubMed

Yoon, Jung-Hoon; Kang, So-Jung; Jung, Yong-Taek; Oh, Tae-Kwang

2010-01-01

A Gram-negative, non-motile and pleomorphic bacterial strain, SMK-114(T), which belongs to the class Alphaproteobacteria, was isolated from a tidal flat sample collected in Byunsan, Korea. Strain SMK-114(T) grew optimally at pH 7.0-8.0 and 25-30 degrees C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SMK-114(T) formed a cluster with Octadecabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 95.2-95.4 %. This cluster was part of the clade comprising Thalassobius species with a bootstrap resampling value of 76.3 %. Strain SMK-114(T) exhibited 16S rRNA gene sequence similarity values of 95.1-96.3 % to members of the genus Thalassobius. It contained Q-10 as the predominant ubiquinone and C(18 : 1)omega7c as the major fatty acid. The DNA G+C content was 60.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-114(T) is considered to represent a novel species in a new genus for which the name Gaetbulicola byunsanensis gen. nov., sp. nov. is proposed. The type strain of Gaetbulicola byunsanensis is SMK-114(T) (=KCTC 22632(T) =CCUG 57612(T)).

Draft genome of Kocuria polaris CMS 76or(T) isolated from cyanobacterial mats, McMurdo Dry Valley, Antarctica: an insight into CspA family of proteins from Kocuria polaris CMS 76or(T).

PubMed

Gundlapally, Sathyanarayana Reddy; Ara, Srinivas; Sisinthy, Shivaji

2015-10-01

Kocuria polaris strain CMS 76or(T) is a gram-positive, orange-pigmented bacterium isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. It is psychrotolerant, orange pigmented, hydrolyses starch and Tween 80 and reduces nitrate. We report the 3.78-Mb genome of K. polaris strain CMS 76or(T), containing 3416 coding sequences, including one each for 5S rRNA, 23S rRNA, 16S rRNA and 47 tRNA genes, and the G+C content of DNA is 72.8%. An investigation of Csp family of proteins from K. polaris strain CMS 76or(T) indicated that it contains three different proteins of CspA (peg.319, peg.2255 and 2832) and the length varied from 67 to 69 amino acids. The three different proteins contain all the signature amino acids and two RNA binding regions that are characteristic of CspA proteins. Further, the CspA from K. polaris strain CMS 76or(T) was different from CspA of four other species of the genus Kocuria, Cryobacterium roopkundense and E. coli indirectly suggesting the role of CspA of K. polaris strain CMS 76or(T) in psychrotolerant growth of the bacterium.

Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum "Nitrospinae".

PubMed

Spieck, Eva; Keuter, Sabine; Wenzel, Thilo; Bock, Eberhard; Ludwig, Wolfgang

2014-05-01

Nitrite oxidizing bacteria are an integral part of the nitrogen cycle in marine waters, but the knowledge about their diversity is limited. Recently, a high abundance of Nitrospina-like 16S rRNA gene sequences has been detected in oceanic habitats with low oxygen content by molecular methods. Here, we describe a new strain of Nitrospina, which was sampled in 100m depth from the Black Sea. It coexisted with a not-yet cultivated chemoorganotrophic gammaproteobacterium and could be purified by classical isolation methods including Percoll density gradient centrifugation. The new Nitrospina-like bacterium grew lithoautotrophically at 28°C in diluted seawater supplemented with inorganic salts and nitrite. Gram-negative rods were characterized morphologically, physiologically and partly biochemically. The 16S rRNA gene of the new strain of Nitrospina is 97.9% similar to the described species N. gracilis and DNA/DNA hybridization experiments revealed a relatedness of 30.0%. The data from both Nitrospina species and environmental clones were used for an extensive 16S rRNA based phylogenetic study applying high quality filtering. Treeing analyses confirm the newly defined phylum status for "Nitrospinae" [18]. The results of phylogenetic and genotypic analyses support the proposal of a novel species Nitrospina watsonii sp. nov. (type strain 347(T), LMG 27401(T), NCIMB 14887(T)). Copyright © 2014 Elsevier GmbH. All rights reserved.

Trophic effect of bombesin on the rat pancreas: is it mediated by the release of gastrin or cholecystokinin?

PubMed

Lhoste, E; Aprahamian, M; Pousse, A; Hoeltzel, A; Stock-Damge, C

1985-01-01

This work investigates the effect, on the rat pancreas, of a chronic administration of bombesin in function of the dose and duration of treatment and examines whether this effect may be mediated by the release of endogenous gastrin or cholecystokinin. Bombesin, administered three times daily for 5 or 15 days, induced a marked increase in pancreatic weight, its protein, RNA and enzyme contents with the dose of 10 micrograms/kg body weight; the ratios of pancreatic weight, protein and RNA contents to DNA contents increased significantly after a 5 day treatment, suggesting cellular hypertrophy. Pancreatic DNA content was markedly enhanced after a 15 day treatment, suggesting cellular hyperplasia. Antrectomy decreased plasma gastrin levels, but did not alter the pancreatico-trophic action of a 10 micrograms/kg bombesin treatment for 5 days. Proglumide, an inhibitor of cholecystokinin and gastrin in the pancreas, did not affect the growth of the pancreas induced by a 10 micrograms/kg bombesin treatment for 5 days. It is concluded that chronic bombesin induces, in the rat pancreas, cellular hypertrophy or hyperplasia depending on the duration of treatment. Pancreatic hypertrophy is not mediated by the release of endogenous gastrin or cholecystokinin.

Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae).

PubMed

Meng, Xiangli; Wang, Yiting; Lu, Shan; Lai, Xin-He; Jin, Dong; Yang, Jing; Xu, Jianguo

2017-09-01

Two strains (pika_113T and pika_114) of a previously undescribed Actinomyces-like bacterium were recovered from the intestinal contents of plateau pika (Ochotona curzoniae) on the Tibet-Qinghai Plateau, China. Results from biochemical characterization indicated that the two strains were phenotypically homogeneous and distinct from other previously described species of the genus Actinomyces. Based on the comparison of 16S rRNA gene sequences and genome analysis, the bacteria were determined to be a hitherto unknown subline within the genus Actinomyces, being most closely related to type strains of Actinomyces denticolens and Actinomyces timonensis with a respective 97.2 and 97.1 % similarity in their 16S rRNA gene sequences. Phylogenetic analyses confirmed that pika_113T was well separated from any other recognized species of the genus Actinomyces and within the cluster with A. denticolens and A. timonensis. The genome of strain pika_113T displayed less than 42 % relatedness in DNA-DNA hybridization with all the available genomes of existing species of the genus Actinomyces in the NCBI database. Collectively, based on the phenotypic characteristics and phylogenetic analyses results, we propose the novel isolates as representatives of Actinomyces gaoshouyii sp. nov. The type strain of Actinomyces gaoshouyii is pika_113T (=CGMCC 4.7372T=DSM 104049T), with a genomic DNA G+C content of 71 mol%.

Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers

PubMed Central

Graf, Louis; Kim, Yae Jin; Cho, Ga Youn; Miller, Kathy Ann

2017-01-01

Coccophora langsdorfii (Turner) Greville (Fucales) is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that should be tested in a large survey of populations of C. langsdorfii. PMID:29095864

Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture.

PubMed

Sundset, Monica A; Edwards, Joan E; Cheng, Yan Fen; Senosiain, Roberto S; Fraile, Maria N; Northwood, Korinne S; Praesteng, Kirsti E; Glad, Trine; Mathiesen, Svein D; Wright, André-Denis G

2009-02-01

The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.

Limnobacter litoralis sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter.

PubMed

Lu, Hongsheng; Sato, Yoshinori; Fujimura, Reiko; Nishizawa, Tomoyasu; Kamijo, Takashi; Ohta, Hiroyuki

2011-02-01

A Gram-negative, aerobic, heterotrophic bacterium, designated KP1-19(T), was isolated from a 22-year-old volcanic deposit at a site lacking vegetation on the island of Miyake, Japan. Strain KP1-19(T) was able to use thiosulfate (optimum concentration 10 mM) as an additional energy source. 16S rRNA gene sequence analysis indicated that strain KP1-19(T) was closely related to Limnobacter thiooxidans CS-K2(T) within the class Betaproteobacteria (97.7 % 16S rRNA gene sequence similarity). The cellular fatty acid profile was characteristic of the genus Limnobacter: the major fatty acids (>5 %) were C(16 : 0), C(16 : 1)ω7c and C(18 : 1)ω7c and minor amounts of C(10 : 0) 3-OH were also found. DNA-DNA relatedness between strain KP1-19(T) and L. thiooxidans LMG 19593(T) was 18 %. Therefore, strain KP1-19(T) represents a novel species, for which the name Limnobacter litoralis sp. nov. is proposed. The type strain is KP1-19(T) (=LMG 24869(T) =NBRC 105857(T) =CIP 109929(T)).

Life cycle as a stable trait in the evaluation of diversity of Nostoc from biofilms in rivers.

PubMed

Mateo, Pilar; Perona, Elvira; Berrendero, Esther; Leganés, Francisco; Martín, Marta; Golubić, Stjepko

2011-05-01

The diversity within the genus Nostoc is still controversial and more studies are needed to clarify its heterogeneity. Macroscopic species have been extensively studied and discussed; however, the microscopic forms of the genus, especially those from running waters, are poorly known and likely represented by many more species than currently described. Nostoc isolates from biofilms of two Spanish calcareous rivers were characterized comparing the morphology and life cycle in two culture media with different levels of nutrients and also comparing the 16S rRNA gene sequences. The results showed that trichome shape and cellular dimensions varied considerably depending on the culture media used, whereas the characteristics expressed in the course of the life cycle remained stable for each strain independent of the culture conditions. Molecular phylogenetic analysis confirmed the distinction between the studied strains established on morphological grounds. A balanced approach to the evaluation of diversity of Nostoc in the service of autecological studies requires both genotypic information and the evaluation of stable traits. The results of this study show that 16S rRNA gene sequence similarity serves as an important criterion for characterizing Nostoc strains and is consistent with stable attributes, such as the life cycle. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample.

PubMed

Renvoise, Aurélie; Raoult, Didier; Roux, Véronique

2010-07-01

Gram-positive, non-spore-forming rods were isolated from a human osteo-articular sample (strain 7400942(T)). Based on cellular morphology and the results of biochemical analysis, this strain was tentatively identified as a novel species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the bacterium was closely related to the type strain of Actinomyces denticolens (96.9 % 16S rRNA gene sequence similarity). A comparison of biochemical traits showed that strain 7400942(T) was distinct from A. denticolens in a number of characteristics, i.e. in contrast with A. denticolens, strain 7400942(T) was negative for nitrate reduction and for beta-galactosidase, alpha-glucosidase and alanine arylamidase activities, it was positive for acid production from N-acetylglucosamine, melezitose and glycogen, and it was negative for acid production from turanose. Matrix-assisted laser-desorption/ionization time-of-flight MS protein analysis confirmed that strain 7400942(T) represents a novel species, as scores obtained for its spectra were significant (>2.2) only with strain 7400942(T). On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain should be designated Actinomyces timonensis sp. nov.; the type strain is strain 7400942(T) (=CSUR P35(T)=CCUG 55928(T)).

New Insights into the RNA-Based Mechanism of Action of the Anticancer Drug 5′-Fluorouracil in Eukaryotic Cells

PubMed Central

Mojardín, Laura; Botet, Javier; Quintales, Luis; Moreno, Sergio; Salas, Margarita

2013-01-01

5-Fluorouracil (5FU) is a chemotherapeutic drug widely used in treating a range of advanced, solid tumours and, in particular, colorectal cancer. Here, we used high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5FU in the eukaryotic model Schizosaccharomyces pombe. This approach combined with real-time quantitative PCR analysis allowed us to detect splicing defects of a significant number of intron-containing mRNA, in addition to identify some rRNA and tRNA processing defects after 5FU treatment. Interestingly, our studies also revealed that 5FU specifically induced the expression of certain genes implicated in the processing of mRNA, tRNA and rRNA precursors, and in the post-transcriptional modification of uracil residues in RNA. The transcription of several tRNA genes was also significantly induced after drug exposure. These transcriptional changes might represent a cellular response mechanism to counteract 5FU damage since deletion strains for some of these up-regulated genes were hypersensitive to 5FU. Moreover, most of these RNA processing genes have human orthologs that participate in conserved pathways, suggesting that they could be novel targets to improve the efficacy of 5FU-based treatments. PMID:24223771

Nuclear distribution of the Trypanosoma cruzi RNA Pol I subunit RPA31 during growth and metacyclogenesis, and characterization of its nuclear localization signal.

PubMed

Canela-Pérez, Israel; López-Villaseñor, Imelda; Cevallos, Ana María; Hernández, Roberto

2018-03-01

Trypanosoma cruzi is the aetiologic agent of Chagas disease. Our research group studies ribosomal RNA (rRNA) gene transcription and nucleolus dynamics in this species of trypanosomes. RPA31 is an essential subunit of RNA polymerase I (Pol I) whose presence is apparently restricted to trypanosomes. Using fluorescent-tagged versions of this protein (TcRPA31-EGFP), we describe its nuclear distribution during growth and metacyclogenesis. Our findings indicate that TcRPA31-EGFP alters its nuclear presence from concentrated nucleolar localization in exponentially growing epimastigotes to a dispersed granular distribution in the nucleoplasm of stationary epimastigotes and metacyclic trypomastigotes. These changes likely reflect a structural redistribution of the Pol I transcription machinery in quiescent cellular stages where downregulation of rRNA synthesis is known to occur. In addition, and related to the nuclear internalization of this protein, the presence of a classical bipartite-type nuclear localization signal was identified towards its C-terminal end. The functionality of this motif was demonstrated by its partial or total deletion in recombinant versions of the tagged fluorescent protein. Moreover, ivermectin inhibited the nuclear localization of the labelled chimaera, suggesting the involvement of the importin α/β transport system.

Streptococcus ovuberis sp. nov., isolated from a subcutaneous abscess in the udder of a sheep.

PubMed

Zamora, Leydis; Pérez-Sancho, Marta; Fernández-Garayzábal, Jose Francisco; Orden, Jose Antonio; Domínguez-Bernal, Gustavo; de la Fuente, Ricardo; Domínguez, Lucas; Vela, Ana Isabel

2017-11-01

One unidentified, Gram-stain-positive, catalase-negative coccus-shaped organism was recovered from a subcutaneous abscess of the udder of a sheep and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria, the isolate was tentatively assigned to the genus Streptococcus, although the organism did not appear to match any recognized species. 16S rRNA gene sequence comparison studies confirmed its identification as a member of the genus Streptococcus and showed that the nearest phylogenetic relatives of the unknown coccus corresponded to Streptococcus moroccensis and Streptococcus cameli (95.9 % 16S rRNA gene sequence similarity). The sodA sequence analysis showed less than 89.3 % sequence similarity with the currently recognized species of the genus Streptococcus. The novel bacterial isolate was distinguished from close relatives of the genus Streptococcusby using biochemical tests. A mass spectrometry profile was also obtained for the novel isolate using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a representative of a novel species of the genus Streptococcus, Streptococcus ovuberis sp. nov. The type strain of Streptococcus ovuberissp. nov. is VB15-00779 T (=CECT 9179 T =CCUG 69612 T ).

Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker.

PubMed

Li, Yong; Xue, Han; Sang, Sheng-Qi; Lin, Cai-Li; Wang, Xi-Zhuo

2017-01-01

Two Gram-stain negative aerobic bacterial strains were isolated from the bark tissue of Populus × euramericana. The novel isolates were investigated using a polyphasic approach including 16S rRNA gene sequencing, genome sequencing, average nucleotide identity (ANI) and both phenotypic and chemotaxonomic assays. The genome core gene sequence and 16S rRNA gene phylogenies suggest that the novel isolates are different from the genera Snodgrassella and Stenoxybacter. Additionally, the ANI, G+C content, main fatty acids and phospholipid profile data supported the distinctiveness of the novel strain from genus Snodgrassella. Therefore, based on the data presented, the strains constitute a novel species of a novel genus within the family Neisseriaceae, for which the name Populibacter corticis gen. nov., sp. nov. is proposed. The type strain is 15-3-5T (= CFCC 13594T = KCTC 42251T).

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts

NASA Technical Reports Server (NTRS)

Woese, C. R.; Achenbach, L.; Rouviere, P.; Mandelco, L.

1991-01-01

A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota.

PubMed

Chassard, Christophe; Delmas, Eve; Robert, Céline; Lawson, Paul A; Bernalier-Donadille, Annick

2012-01-01

A strictly anaerobic, cellulolytic strain, designated 18P13(T), was isolated from a human faecal sample. Cells were Gram-positive non-motile cocci. Strain 18P13(T) was able to degrade microcrystalline cellulose but the utilization of soluble sugars was restricted to cellobiose. Acetate and succinate were the major end products of cellulose and cellobiose fermentation. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Ruminococcus of the family Ruminococcaceae. The closest phylogenetic relative was the ruminal cellulolytic strain Ruminococcus flavefaciens ATCC 19208(T) (<95% 16S rRNA gene sequence similarity). The DNA G+C content of strain 18P13(T) was 53.05±0.7 mol%. On the basis of phylogenetic analysis, and morphological and physiological data, strain 18P13(T) can be differentiated from other members of the genus Ruminococcus with validly published names. The name Ruminococcus champanellensis sp. nov. is proposed, with 18P13(T) (=DSM 18848(T)=JCM 17042(T)) as the type strain.

Cellular metabolic rates from primary dermal fibroblast cells isolated from birds of different body masses.

PubMed

Jimenez, Ana Gabriela; Williams, Joseph B

2014-10-01

The rate of metabolism is the speed at which organisms use energy, an integration of energy transformations within the body; it governs biological processes that influence rates of growth and reproduction. Progress at understanding functional linkages between whole organism metabolic rate and underlying mechanisms that influence its magnitude has been slow despite the central role this issue plays in evolutionary and physiological ecology. Previous studies that have attempted to relate how cellular processes translate into whole-organism physiology have done so over a range of body masses of subjects. However, the data still remains controversial when observing metabolic rates at the cellular level. To bridge the gap between these ideas, we examined cellular metabolic rate of primary dermal fibroblasts isolated from 49 species of birds representing a 32,000-fold range in body masses to test the hypothesis that metabolic rate of cultured cells scales with body size. We used a Seahorse XF-96 Extracellular flux analyzer to measure cellular respiration in fibroblasts. Additionally, we measured fibroblast size and mitochondrial content. We found no significant correlation between cellular metabolic rate, cell size, or mitochondrial content and body mass. Additionally, there was a significant relationship between cellular basal metabolic rate and proton leak in these cells. We conclude that metabolic rate of cells isolated in culture does not scale with body mass, but cellular metabolic rate is correlated to growth rate in birds. Copyright © 2014 Elsevier Inc. All rights reserved.

High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles.

PubMed

Li, Fuhai; Zhou, Xiaobo; Zhu, Jinmin; Ma, Jinwen; Huang, Xudong; Wong, Stephen T C

2007-10-09

High content screening (HCS)-based image analysis is becoming an important and widely used research tool. Capitalizing this technology, ample cellular information can be extracted from the high content cellular images. In this study, an automated, reliable and quantitative cellular image analysis system developed in house has been employed to quantify the toxic responses of human H4 neuroglioma cells exposed to metal oxide nanoparticles. This system has been proved to be an essential tool in our study. The cellular images of H4 neuroglioma cells exposed to different concentrations of CuO nanoparticles were sampled using IN Cell Analyzer 1000. A fully automated cellular image analysis system has been developed to perform the image analysis for cell viability. A multiple adaptive thresholding method was used to classify the pixels of the nuclei image into three classes: bright nuclei, dark nuclei, and background. During the development of our image analysis methodology, we have achieved the followings: (1) The Gaussian filtering with proper scale has been applied to the cellular images for generation of a local intensity maximum inside each nucleus; (2) a novel local intensity maxima detection method based on the gradient vector field has been established; and (3) a statistical model based splitting method was proposed to overcome the under segmentation problem. Computational results indicate that 95.9% nuclei can be detected and segmented correctly by the proposed image analysis system. The proposed automated image analysis system can effectively segment the images of human H4 neuroglioma cells exposed to CuO nanoparticles. The computational results confirmed our biological finding that human H4 neuroglioma cells had a dose-dependent toxic response to the insult of CuO nanoparticles.

Meatal Swabs Contain Less Cellular Material and Are Associated with a Decrease in Gram Stain Smear Quality Compared to Urethral Swabs in Men.

PubMed

Jordan, Stephen J; Schwebke, Jane R; Aaron, Kristal J; Van Der Pol, Barbara; Hook, Edward W

2017-07-01

Urethral swabs are the samples of choice for point-of-care Gram stain testing to diagnose Neisseria gonorrhoeae infection and nongonococcal urethritis (NGU) in men. As an alternative to urethral swabs, meatal swabs have been recommended for the collection of urethral discharge to diagnose N. gonorrhoeae and Chlamydia trachomatis infection in certain populations by nucleic acid amplification testing (NAAT), as they involve a less invasive collection method. However, as meatal swabs could be sampling a reduced surface area and result in fewer collected epithelial cells compared to urethral swabs, the adequacy of meatal swab specimens to collect sufficient cellular material for Gram stain testing remains unknown. We enrolled 66 men who underwent either urethral or meatal swabbing and compared the cellular content and Gram stain failure rate. We measured the difference in swab cellular content using the Cepheid Xpert CT/NG sample adequacy control crossing threshold (SAC CT ) and determined the failure rate of Gram stain smears (GSS) due to insufficient cellular material. In the absence of discharge, meatal smears were associated with a significant reduction in cellular content ( P = 0.0118), which corresponded with a GSS failure rate significantly higher than that for urethral swabs (45% versus 3%, respectively; P < 0.0001). When discharge was present, there was no difference among results from urethral and meatal swabs. Therefore, if GSS testing is being considered for point-of-care diagnosis of N. gonorrhoeae infection or NGU in men, meatal swabs should be avoided in the absence of a visible discharge. Copyright © 2017 American Society for Microbiology.

Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria

PubMed Central

Jackson, Christopher J; Norman, John E; Schnare, Murray N; Gray, Michael W; Keeling, Patrick J; Waller, Ross F

2007-01-01

Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs) within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes. Results From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression. Conclusion The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements within the genome, RNA editing, loss of stop codons, and use of trans-splicing. PMID:17897476

Increased 5S rRNA oxidation in Alzheimer's disease.

PubMed

Ding, Qunxing; Zhu, Haiyan; Zhang, Bing; Soriano, Augusto; Burns, Roxanne; Markesbery, William R

2012-01-01

It is widely accepted that oxidative stress is involved in neurodegenerative disorders such as Alzheimer's disease (AD). Ribosomal RNA (rRNA) is one of the most abundant molecules in most cells and is affected by oxidative stress in the human brain. Previous data have indicated that total rRNA levels were decreased in the brains of subjects with AD and mild cognitive impairment concomitant with an increase in rRNA oxidation. In addition, level of 5S rRNA, one of the essential components of the ribosome complex, was significantly lower in the inferior parietal lobule (IP) brain area of subjects with AD compared with control subjects. To further evaluate the alteration of 5S rRNA in neurodegenerative human brains, multiple brain regions from both AD and age-matched control subjects were used in this study, including IP, superior and middle temporal gyro, temporal pole, and cerebellum. Different molecular pools including 5S rRNA integrated into ribosome complexes, free 5S rRNA, cytoplasmic 5S rRNA, and nuclear 5S rRNA were studied. Free 5S rRNA levels were significantly decreased in the temporal pole region of AD subjects and the oxidation of ribosome-integrated and free 5S rRNA was significantly increased in multiple brain regions in AD subjects compared with controls. Moreover, a greater amount of oxidized 5S rRNA was detected in the cytoplasm and nucleus of AD subjects compared with controls. These results suggest that the increased oxidation of 5S rRNA, especially the oxidation of free 5S rRNA, may be involved in the neurodegeneration observed in AD.

Evaluation of the Efficiency of the Reticulocyte Hemoglobin Content on Diagnosis for Iron Deficiency Anemia in Chinese Adults.

PubMed

Cai, Jie; Wu, Meng; Ren, Jie; Du, Yali; Long, Zhangbiao; Li, Guoxun; Han, Bing; Yang, Lichen

2017-05-02

Our aim was to evaluate the cut-off value and efficiency of using reticulocyte hemoglobin content as a marker to diagnose iron deficiency anemia in Chinese adults. 140 adults who needed bone marrow aspiration for diagnosis at the hematology department of the Peking Union Medical College Hospital were enrolled according to the inclusive and exclusive criteria. Venous blood samples were collected to detect complete blood count, including hemoglobin, reticulocyte hemoglobin content, hematocrit, mean cellular volume, corpuscular hemoglobin concentration, hemoglobin content, free erythrocyte protoporphyrin; iron indexes of serum ferritin, serum transferrin receptor, and unsaturated iron-binding capacity; and inflammation markers of C-reactive protein and α-acid glycoprotein. Bone marrow samples were obtained for the bone marrow iron staining, which was used as the standard for the evaluation of iron status in this study. Subjects were divided into three groups according to hemoglobin levels and bone marrow iron staining results: the IDA (iron deficiency anemia) group, the NIDA (non-iron deficiency anemia) group, and the control group. The differences of the above-mentioned indexes were compared among the three groups and the effect of inflammation was also considered. The cut-off value of reticulocyte hemoglobin content was determined by receiver operation curves. The IDA group ( n = 56) had significantly lower reticulocyte hemoglobin content, mean cellular volume, corpuscular hemoglobin concentration, hemoglobin content, and serum ferritin; and higher free erythrocyte protoporphyrin, unsaturated iron-binding capacity, and serum transferrin receptor ( p < 0.05) compared with the NIDA group ( n = 38) and control group ( n = 46). Hematocrit, serum ferritin, and unsaturated iron-binding capacity were significantly affected by inflammation while reticulocyte hemoglobin content and other parameters were not. The cut-off value of reticulocyte hemoglobin content for diagnosing iron deficiency anemia was 27.2 pg, with a sensitivity of 87.5% and a specificity of 92.9%. The cut-off values for mean cellular volume, serum ferritin, and serum transferrin receptor were 76.6, 12.9, and 4.89 mg/L, respectively. Reticulocyte hemoglobin content had the largest area under the curve of 0.929, while those for mean cellular volume, serum ferritin, serum transferrin receptor were 0.922, 0.887, and 0.900, respectively. Reticulocyte hemoglobin content has a high sensitivity and specificity in the diagnosis of iron deficiency anemia, and its comprehensive diagnostic efficacy is better than other traditional indicators-such as serum ferritin and serum transferrin receptor.

Identification of Circular RNAs from the Parental Genes Involved in Multiple Aspects of Cellular Metabolism in Barley

PubMed Central

Darbani, Behrooz; Noeparvar, Shahin; Borg, Søren

2016-01-01

RNA circularization made by head-to-tail back-splicing events is involved in the regulation of gene expression from transcriptional to post-translational levels. By exploiting RNA-Seq data and down-stream analysis, we shed light on the importance of circular RNAs in plants. The results introduce circular RNAs as novel interactors in the regulation of gene expression in plants and imply the comprehensiveness of this regulatory pathway by identifying circular RNAs for a diverse set of genes. These genes are involved in several aspects of cellular metabolism as hormonal signaling, intracellular protein sorting, carbohydrate metabolism and cell-wall biogenesis, respiration, amino acid biosynthesis, transcription and translation, and protein ubiquitination. Additionally, these parental loci of circular RNAs, from both nuclear and mitochondrial genomes, encode for different transcript classes including protein coding transcripts, microRNA, rRNA, and long non-coding/microprotein coding RNAs. The results shed light on the mitochondrial exonic circular RNAs and imply the importance of circular RNAs for regulation of mitochondrial genes. Importantly, we introduce circular RNAs in barley and elucidate their cellular-level alterations across tissues and in response to micronutrients iron and zinc. In further support of circular RNAs' functional roles in plants, we report several cases where fluctuations of circRNAs do not correlate with the levels of their parental-loci encoded linear transcripts. PMID:27375638

Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)▿

PubMed Central

Evans, Paul N.; Hinds, Lyn A.; Sly, Lindsay I.; McSweeney, Christopher S.; Morrison, Mark; Wright, André-Denis G.

2009-01-01

The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight. PMID:19218421

Whole genome sequences and annotation of Micrococcus luteus SUBG006, a novel phytopathogen of mango.

PubMed

Rakhashiya, Purvi M; Patel, Pooja P; Thaker, Vrinda S

2015-12-01

Actinobaceria, Micrococcus luteus SUBG006 was isolated from infected leaves of Mangifera indica L. vr. Nylon in Rajkot, (22.30°N, 70.78°E), Gujarat, India. The genome size is 3.86 Mb with G + C content of 69.80% and contains 112 rRNA sequences (5S, 16S and 23S). The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JOKP00000000.

Roseovarius indicus sp. nov., isolated from deep-sea water of the Indian Ocean.

PubMed

Lai, Qiliang; Zhong, Huanzi; Wang, Jianning; Yuan, Jun; Sun, Fengqin; Wang, Liping; Zheng, Tianling; Shao, Zongze

2011-09-01

A taxonomic study was carried out on a novel bacterial strain, designated B108(T), which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium, enriched from deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped and non-motile. Growth of strain B108(T) was observed in 1-15 % (w/v) NaCl and at 10-39 °C and it was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence comparisons showed that strain B108(T) was most closely related to Roseovarius halotolerans HJ50(T) (97.1 % sequence similarity), followed by Roseovarius pacificus 81-2(T) (96.6 %) and Roseovarius aestuarii SMK-122(T) (95.2 %); other species shared <95.0 % sequence similarity. DNA-DNA hybridization tests showed that strain B108(T) had a low DNA-DNA relatedness to R. halotolerans HJ50(T) and R. pacificus 81-2(T) (48±4 % and 44±5 %, respectively). The predominant fatty acids were C₁₆:₀, C₁₆:₀ 2-OH, summed feature 8 (C₁₈:₁ω7c/ω6c) and C₁₉:₀ω8c cyclo, which accounted for 84.2 % of the total cellular fatty acids. The G+C content of the chromosomal DNA was 63.6 mol%. The major respiratory quinone was ubiquinone 10 (Q10). Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and some unidentified compounds were detected. These characteristics were in good agreement with those of members of the genus Roseovarius. The pufLM gene was also detected. According to its morphology, physiology, fatty acid composition and phylogenetic position based on 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Roseovarius but can be readily distinguished from known species of this genus. Therefore, strain B108(T) represents a novel species, of the genus Roseovarius, for which the name Roseovarius indicus sp. nov. is proposed. The type strain is B108(T) ( = 2PR52-14(T)  = CCTCC AB 208233(T)  = LMG 24622(T)  = MCCC 1A01227(T)).

Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root.

PubMed

Qiu, Fubin; Zhang, Xiaoxia; Liu, Lin; Sun, Lei; Schumann, Peter; Song, Wei

2009-04-01

Four alkaligenous, moderately halotolerant strains, designated ge09, ge10(T), ge14(T) and ge15, were isolated from the internal tissue of ginseng root and their taxonomic positions were investigated by using a polyphasic approach. Cells of the four strains were Gram-positive-staining, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains ge09 and ge10(T) formed one cluster and strains ge14(T) and ge15 formed another separate cluster within the genus Bacillus. 16S rRNA gene sequence similarities with type strains of other Bacillus species were less than 97 %. Levels of DNA-DNA relatedness among the four strains showed that strains ge09 and ge10(T) and strains ge14(T) and ge15 belonged to two separate species; the mean level of DNA-DNA relatedness between ge10(T) and ge14(T) was only 28.7 %. Their phenotypic and physiological properties supported the view that the two strains represent two different novel species of the genus Bacillus. The DNA G+C contents of strains ge10(T) and ge14(T) were 49.9 and 49.6 mol%, respectively. Strains ge10(T) and ge14(T) showed the peptidoglycan type A4alpha l-Lys-d-Glu. The lipids present in strains ge10(T) and ge14(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. Their predominant respiratory quinone was MK-7. The fatty acid profiles of the four novel strains contained large quantities of branched and saturated fatty acids. The predominant cellular fatty acids were iso-C(15 : 0) (42.5 %), anteiso-C(15 : 0) (22.2 %), anteiso-C(17 : 0) (7.3 %) and C(16 : 1)omega7c alcohol (5.7 %) in ge10(T) and iso-C(15 : 0) (50.7 %) and anteiso-C(15 : 0) (20.1 %) in ge14(T). On the basis of their phenotypic properties and phylogenetic distinctiveness, two novel species of the genus Bacillus are proposed, Bacillus beijingensis sp. nov. (type strain ge10(T) =DSM 19037(T) =CGMCC 1.6762(T)) and Bacillus ginsengi sp. nov. (type strain ge14(T) =DSM 19038(T) =CGMCC 1.6763(T)).

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns.

PubMed

López-Hermoso, Clara; de la Haba, Rafael R; Sánchez-Porro, Cristina; Ventosa, Antonio

2018-05-01

Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184 T , IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAG T (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508 T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472 T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182 T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184 T were C 16:0 and C 18:1 . The DNA G+C content range was 51.9-52.5mol% (T m ) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184 T (=CECT 9177 T =LMG 29817 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench.

PubMed

Wei, Yuli; Mao, Haiyan; Xu, Yunping; Zou, Wencai; Fang, Jiasong; Blom, Jochen

2018-06-21

A novel heterotrophic, Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain MT5 T , was isolated from deep seawater in the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range, 4-45 °C), pH 5-7 (pH 4-11) and with 3-7 % (w/v) NaCl (0-18 %). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MT5 T was related to members of the genus Pseudomonas and shared the highest sequence identities with Pseudomonas pachastrellae CCUG 46540 T (99.6 %), Pseudomonas aestusnigri VGXO14 T (98.5 %) and Pseudomonas oceani KX 20 T (98.4 %). The 16S rRNA gene sequence identities between strain MT5 T and other members of the genus Pseudomonas were below 96.7 %. The digital DNA-DNA hybridization values between strain MT5 T and the two type strains, P. pachastrellae and P. aestusnigri, were 38.9±2.5 and 25.8±2.4 %, respectively. The average nucleotide identity values between strain MT5 T and the two type strains were 90.3 and 87.0 %, respectively. Strain MT5 T and the two type strains shared 94.98 and 86.2 % average amino acid identity, and 30 and 33 Karlin genomic signature, respectively. The sole respiratory menaquinone was Q-9. The major polar lipids were phosphatidylethanolamine, diphosphatidyglycerol and phosphatidylglycerol. The predominant cellular fatty acids of strain MT5 T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (35.3 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (24.1 %), C16 : 0 (15.9 %) and C12 : 0 (7.2 %). The G+C content of the genomic DNA was 61.2 mol%. The combined genotypic and phenotypic data indicated that strain MT5 T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas abyssi sp. nov. is proposed, with the type strain MT5 T (=KCTC 62295 T =MCCC 1K03351 T ).

Altered gravity influences rDNA and NopA100 localization in nucleoli

NASA Astrophysics Data System (ADS)

Sobol, M. A.; Kordyum, E. L.

Fundamental discovery of gravisensitivity of cells no specified to gravity perception focused increasing attention on an elucidation of the mechanisms involved in altered gravity effects at the cellular and subcellular levels. The nucleolus is the transcription site of rRNA genes as well as the site of processing and initial packaging of their transcripts with ribosomal and nonribosomal proteins. The mechanisms inducing the changes in the subcomponents of the nucleolus that is morphologically defined yet highly dynamic structure are still unknown in detail. To understand the functional organization of the nucleolus as in the control as under altered gravity conditions it is essential to determine both the precise location of rDNA and the proteins playing the key role in rRNA processing. Lepidium sativum seeds were germinated in 1% agar medium on the slow horizontal clinostat (2 rpm) and in the stationary conditions. We investigated the root meristematic cells dissected from the seedlings grown in darkness for two days. The investigations were carried out with anti-DNA and anti-NopA100 antibodies labeling as well as with TdT procedure, and immunogold electron microscopy. In the stationary growth conditions, the anti-DNA antibody as well TdT procedure were capable of detecting fibrillar centers (FCs) and the dense fibrillar component (DFC) in the nucleolus. In FCs, gold particles were revealed on the condensed chromatin inclusions, internal fibrils of decondensed rDNA and the transition zone FC-DFC. Quantitatively, FCs appeared 1,5 times more densely labeled than DFC. NopA100 was localized in FCs and in DFC. In FCs, the most of protein was revealed in the transition zone FC-DFC. After a quantitative study, FCs and the transition zone FC-DFC appeared to contain NopA100 1,7 times more than DFC. Under the conditions of altered gravity, quantitative data clearly showed a redistribution of nucleolar DNA and NopA100 between FCs and DFC in comparison with the control. In labeling both with anti-DNA antibody and by TdT method, 1,5 times more gold particles were localized on FCs, and 1,5 times less in DFC. Unlike the control, condensed r-chromatin blocks and inner rDNA were labeled much more than the transition zone FC-DFC in fibrillar centers. The content of NopA100 in FCs and the transition zone FC-DFC was 2,4 times more than in the control. Twice less quantity of the protein was revealed in DFC as compared to the control. In fibrillar centers, the majority of NopA100 was localized in the inner space of FCs than in the transition zone FC-DFC. Re-localization of rDNA and NopA100 in the nucleolar subcomponents indicates lowering the level of rDNA transcription as well as middle and late processing of rRNA that let us to propose lowering the functional activity of the nucleolus under the influence of altered gravity.

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

NASA Astrophysics Data System (ADS)

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-04-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue.

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

PubMed Central

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-01-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue. PMID:27063397

A new Microbacterium species isolated from the blood of a patient with fever: Microbacterium pyrexiae sp. nov.

PubMed

Ko, Kwan Soo; Oh, Won Sup; Lee, Mi Young; Peck, Kyong Ran; Lee, Nam Yong; Song, Jae-Hoon

2007-04-01

A Gram-positive bacterium, SMC-A8265(T), which was isolated from the blood of a patient with fever but could not be identified by a conventional microbiologic method, was finally characterized by performing phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain SMC-A8265(T) belonged to the genus Microbacterium, but it did not correspond to any of the previously described Microbacterium spp. Biochemical tests and cellular fatty acid composition analysis also confirmed that this bacterium is distinct from other Microbacterium spp. Based on the phenotypic and genotypic characteristics, we propose that the strain SMC-A8265(T) should be classified as a new species, namely, Microbacterium pyrexiae sp. nov.

Biochemical and physiological responses of halophilic nanophytoplankton (Dunaliella salina) from exposure to xeno-estrogen 17α-ethinylestradiol.

PubMed

Belhaj, Dalel; Athmouni, Khaled; Frikha, Doniez; Kallel, Monem; El Feki, Abdelfattah; Maalej, Sami; Zhou, John L; Ayadi, Habib

2017-03-01

The environmental impacts of various pollutants on the entire levels of organisms are under investigation. Among these pollutants, endocrine-disrupting compounds (EDCs) present a serious hazard, even though the environmental significance of these compounds remains basically unknown. To drop some light on this field, we assessed the effects of a 11-day exposure of 17α-ethinylestradiol (EE2) on the growth, metabolic content, antioxidant response, oxidative stress, and genetic damage of Dunaliella salina, isolated from Tunisian biotopes. The results showed that at 10 ng L -1 , EE2 could stimulate the growth of D. salina and increase its cellular content of photosynthetic pigments and metabolites; however, it did not significantly increase the activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) or the level of malondialdehyde (MDA) and hydrogen peroxide (H 2 O 2 ). In contrast, exposure to high levels of EE2 concentrations significantly inhibited the growth of D. salina (P < 0.05), decreased the cellular content of photosynthetic pigments, increased the cellular content of all of the metabolites and the SOD activity, and inhibited CAT and GPx activities. Nevertheless, the balance between oxidant and antioxidant enzymes was disrupted because H 2 O 2 content along with MDA content simultaneously increased. Contrary to expected results, DNA damage (strand breaks) decreased after the exposure of algae to EE2. The results of this study suggest that EE2 toxicity could result in environmental impacts with consequences on the whole aquatic community. Graphical abstract.

Aestuariicola saemankumensis gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from tidal flat sediment.

PubMed

Yoon, Jung-Hoon; Kang, So-Jung; Jung, Yong-Taek; Oh, Tae-Kwang

2008-09-01

A Gram-negative, non-motile, pleomorphic bacterial strain, designated SMK-142(T), was isolated from a tidal flat of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain SMK-142(T) grew optimally at pH 7.0-8.0, 25 degrees C and in the presence of 2% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SMK-142(T) clustered with Lutibacter litoralis with which it exhibited a 16S rRNA gene sequence similarity value of 91.2%. This cluster joined the clade comprising the genera Tenacibaculum and Polaribacter at a high bootstrap resampling value. Strain SMK-142(T) contained MK-6 as the predominant menaquinone and iso-C(15:0), iso-C(15:1) and iso-C(17:0) 3-OH as the major fatty acids. The DNA G+C content was 37.2 mol%. Strain SMK-142(T) was differentiated from three phylogenetically related genera, Lutibacter, Tenacibaculum and Polaribacter, on the basis of low 16S rRNA gene sequence similarity values and differences in fatty acid profiles and in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-142(T) represents a novel genus and species for which the name Aestuariicola saemankumensis gen. nov., sp. nov. is proposed (phylum Bacteroidetes, family Flavobacteriaceae). The type strain of the type species, Aestuariicola saemankumensis sp. nov., is SMK-142(T) (=KCTC 22171(T)=CCUG 55329(T)).

Pseudoclavibacter caeni sp. nov., isolated from sludge of a sewage disposal plant.

PubMed

Srinivasan, Sathiyaraj; Kim, Hyun Sook; Kim, Myung Kyum; Lee, Myungjin

2012-04-01

A Gram-positive, strictly aerobic, rod-shaped, non-motile bacterial strain, designated MJ28T, was isolated from a sludge sample from the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ28T. Strain MJ28T showed highest 16S rRNA gene sequence similarity to Pseudoclavibacter soli KP02T (95.2 %). Levels of 16S rRNA gene sequence similarity to the type strains of other Pseudoclavibacter species were less than 94.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ28T belonged to the clade formed by members of the genus Pseudoclavibacter in the family Microbacteriaceae. The G+C content of the genomic DNA of strain MJ28T was 65.8 mol%. The chemotaxonomic characteristics of strain MJ28T showed features typical of the genus Pseudoclavibacter, with MK-9 as the predominant respiratory quinone, 2,4-diaminobutryic acid as the diamino acid in the peptidoglycan, and anteiso-C17:0 (44.6 %), anteiso-C15:0 (35.7 %) and C16:0 (9.5 %) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ28T is considered to represent a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter caeni sp. nov. is proposed. The type strain is MJ28T (=KCTC 19773T=JCM 16921T).

Molecular characterization of 5S ribosomal RNA genes and transcripts in the protozoan parasite Leishmania major.

PubMed

Moreno-Campos, Rodrigo; Florencio-Martínez, Luis E; Nepomuceno-Mejía, Tomás; Rojas-Sánchez, Saúl; Vélez-Ramírez, Daniel E; Padilla-Mejía, Norma E; Figueroa-Angulo, Elisa; Manning-Cela, Rebeca; Martínez-Calvillo, Santiago

2016-12-01

Eukaryotic 5S rRNA, synthesized by RNA polymerase III (Pol III), is an essential component of the large ribosomal subunit. Most organisms contain hundreds of 5S rRNA genes organized into tandem arrays. However, the genome of the protozoan parasite Leishmania major contains only 11 copies of the 5S rRNA gene, which are interspersed and associated with other Pol III-transcribed genes. Here we report that, in general, the number and order of the 5S rRNA genes is conserved between different species of Leishmania. While in most organisms 5S rRNA genes are normally associated with the nucleolus, combined fluorescent in situ hybridization and indirect immunofluorescence experiments showed that 5S rRNA genes are mainly located at the nuclear periphery in L. major. Similarly, the tandemly repeated 5S rRNA genes in Trypanosoma cruzi are dispersed throughout the nucleus. In contrast, 5S rRNA transcripts in L. major were localized within the nucleolus, and scattered throughout the cytoplasm, where mature ribosomes are located. Unlike other rRNA species, stable antisense RNA complementary to 5S rRNA is not detected in L. major.

Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine.

PubMed

Benardini, James N; Vaishampayan, Parag A; Schwendner, Petra; Swanner, Elizabeth; Fukui, Youhei; Osman, Sharif; Satomi, Masakata; Venkateswaran, Kasthuri

2011-06-01

A novel Gram-positive, motile, endospore-forming, aerobic bacterium was isolated from the NASA Phoenix Lander assembly clean room that exhibits 100 % 16S rRNA gene sequence similarity to two strains isolated from a deep subsurface environment. All strains are rod-shaped, endospore-forming bacteria, whose endospores are resistant to UV radiation up to 500 J m(-2). A polyphasic taxonomic study including traditional phenotypic tests, fatty acid analysis, 16S rRNA gene sequencing and DNA-DNA hybridization analysis was performed to characterize these novel strains. The 16S rRNA gene sequencing convincingly grouped these novel strains within the genus Paenibacillus as a separate cluster from previously described species. The similarity of 16S rRNA gene sequences among the novel strains was identical but only 98.1 to 98.5 % with their nearest neighbours Paenibacillus barengoltzii ATCC BAA-1209(T) and Paenibacillus timonensis CIP 108005(T). The menaquinone MK-7 was dominant in these novel strains as shown in other species of the genus Paenibacillus. The DNA-DNA hybridization dissociation value was <45 % with the closest related species. The novel strains had DNA G+C contents of 51.9 to 52.8 mol%. Phenotypically, the novel strains can be readily differentiated from closely related species by the absence of urease and gelatinase and the production of acids from a variety of sugars including l-arabinose. The major fatty acid was anteiso-C(15 : 0) as seen in P. barengoltzii and P. timonensis whereas the proportion of C(16 : 0) was significantly different from the closely related species. Based on phylogenetic and phenotypic results, it was concluded that these strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus phoenicis sp. nov. is proposed. The type strain is 3PO2SA(T) ( = NRRL B-59348(T)  = NBRC 106274(T)).

[Isolation and phylogenetic analysis of one actinomycete strain YIM 90022 exhibiting anticancer activity].

PubMed

Chen, Yi-Guang; Li, Wen-Jun; Cui, Xiao-Long; Jiang, Cheng-Lin; Xu, Li-Hua

2006-10-01

One facultative alkaliphilic actinomycete strain YIM 90022 was isolated from hypersaline alkaline soil in Qinghai province, China. An almost-complete 16S rRNA gene sequence (1500 bp) for strain YIM 90022 was obtained. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 90022 was closely related to four members of the genus Nocardiopsis with 16S rRNA gene sequence similarity values of 98.8% (N. exhalans DSM 44407T), 98.5% (N. prasina DSM 43845T), 98.4% (N. metallicus DSM 44598T) and 97.8% (N. listeri DSM 40297T), but represented a distinct phylogenetic lineage. Repetitive element sequence-based PCR (rep-PCR) genomic fingerprinting was evaluated on strain YIM 90022 and its closest relatives to investigate their genetic relatedness. The analysis of the rep-PCR genomic fingerprints showed that strain YIM 90022 was distinguishable from its closest relatives. The polyphasic taxonomic data presented in this study, including its morphology, physiological and biochemical characteristics, chemotaxonomy, 16S rRNA gene sequence-based phylogenetic analysis and rep-PCR genomic fingerprinting, supported the view that strain YIM 90022 represented a potential new species of the genus Nocardiopsis. The fermentation broth of strain YIM 90022 strongly inhibited growth of cell series of gastric cancer, lung cancer, mammary cancer, melanoma cancer, renal cancer and uterus cancer. Strain YIM 90022 grew well on most tested media, producing exuberant vegetative hyphae and aerial hyphae. The vegetative hyphae are long and fragmented. Light yellow to deep brown diffusible pigments were produced on ISP 2, ISP 3 and ISP 6. Growth of the strain occurred in the pH range 6.0-12.0, with optimal pH8.5. The NaCl tolerate range was 0-15% (W/V). Cell walls contain meso-diaminopimelic acid and have no diagnostic sugars. Polar lipids are phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine. Major menaquinones are MK-10 (H4, H6). The DNA G + C content is 71.5 mol %.

Within-Mat Variability in Anatoxin-a and Homoanatoxin-a Production among Benthic Phormidium (Cyanobacteria) Strains

PubMed Central

Wood, Susanna A.; Smith, Francine M. J.; Heath, Mark W.; Palfroy, Thomas; Gaw, Sally; Young, Roger G.; Ryan, Ken G.

2012-01-01

Benthic Phormidium mats can contain high concentrations of the neurotoxins anatoxin-a and homoanatoxin-a. However, little is known about the co-occurrence of anatoxin-producing and non-anatoxin-producing strains within mats. There is also no data on variation in anatoxin content among toxic genotypes isolated from the same mat. In this study, 30 Phormidium strains were isolated from 1 cm2 sections of Phormidium-dominated mats collected from three different sites. Strains were grown to stationary phase and their anatoxin-a, homoanatoxin-a, dihydroanatoxin-a and dihydrohomoanatoxin-a concentrations determined using liquid chromatography-mass spectrometry. Each strain was characterized using morphological and molecular (16S rRNA gene sequences) techniques. Eighteen strains produced anatoxin-a, dihydroanatoxin-a or homoanatoxin-a. Strains isolated from each mat either all produced toxins, or were a mixture of anatoxin and non-anatoxin-producing genotypes. Based on morphology these genotypes could not be separated. The 16S rRNA gene sequence comparisons showed a difference of at least 17 nucleotides among anatoxin and non-anatoxin-producing strains and these formed two separate sub-clades during phylogenetic analysis. The total anatoxin concentration among toxic strains varied from 2.21 to 211.88 mg kg−1 (freeze dried weight), representing a 100 fold variation in toxin content. These data indicate that both the relative abundance of anatoxin and non-anatoxin-producing genotypes, and variations in anatoxin producing capability, can influence the overall toxin concentration of benthic Phormidium mat samples. PMID:23162704

Microbial community structure of relict niter-beds previously used for saltpeter production.

PubMed

Narihiro, Takashi; Tamaki, Hideyuki; Akiba, Aya; Takasaki, Kazuto; Nakano, Koichiro; Kamagata, Yoichi; Hanada, Satoshi; Maji, Taizo

2014-01-01

From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

Shifts in microbial community composition following surface application of dredged river sediments.

PubMed

Baniulyte, Dovile; Favila, Emmanuel; Kelly, John J

2009-01-01

Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In order to determine the effects of this drastic habitat change on sediment microbial communities, we examined sediment physical, chemical, and microbial characteristics at the time of sediment application to the soil surface as well as 1 and 2 years after application. Microbial community biomass was determined by measurement of lipid phosphate. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, and clone library sequencing of 16S rRNA genes. Results indicated that the moisture content, organic carbon, and total nitrogen content of the sediment all decreased over time. Total microbial biomass did not change over the course of the study, but there were significant changes in the composition of the microbial communities. PLFA analysis revealed relative increases in fungi, actinomycetes, and Gram positive bacteria. T-RFLP analysis indicated a significant shift in bacterial community composition within 1 year of application, and clone library analysis revealed relative increases in Proteobacteria, Gemmatimonadetes, and Bacteriodetes and relative decreases in Acidobacteria, Spirochaetes, and Planctomycetes. These results provide insight into microbial community shifts following land application of dredged sediment.

Diversity of ionizing radiation-resistant bacteria obtained from the Taklimakan Desert.

PubMed

Yu, Li Zhi-Han; Luo, Xue-Song; Liu, Ming; Huang, Qiaoyun

2015-01-01

So far, little is known about the diversity of the radiation-resistant microbes of the hyperarid Taklimakan Desert. In this study, ionizing radiation (IR)-resistant bacteria from two sites in Xinjiang were investigated. After exposing the arid (water content of 0.8 ± 0.3%) and non-arid (water content of 21.3 ± 0.9%) sediment samples to IR of 3000 Gy using a (60)Co source, a total of 52 γ-radiation-resistant bacteria were isolated from the desert sample. The 16S rRNA genes of all isolates were sequenced. The phylogenetic tree places these isolates into five groups: Cytophaga-Flavobacterium-Bacteroides, Proteobacteria, Deinococcus-Thermus, Firmicutes, and Actinobacteria. Interestingly, this is the first report of radiation-resistant bacteria belonging to the genera Knoellia, Lysobacter, Nocardioides, Paracoccus, Pontibacter, Rufibacter and Microvirga. The 16s rRNA genes of four isolates showed low sequence similarities to those of the published species. Phenotypic analysis showed that all bacteria in this study are able to produce catalase, suggesting that these bacteria possess reactive oxygen species (ROS)-scavenging enzymes. These radiation-resistant bacteria also displayed diverse metabolic properties. Moreover, their radiation resistances were found to differ. The diversity of the radiation-resistant bacteria in the desert provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of ROS-scavenging systems that protect cells against oxidative damage caused by desiccation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

PubMed

Shiao, Yih-Horng; Lupascu, Sorin T; Gu, Yuhan D; Kasprzak, Wojciech; Hwang, Christopher J; Fields, Janet R; Leighty, Robert M; Quiñones, Octavio; Shapiro, Bruce A; Alvord, W Gregory; Anderson, Lucy M

2009-10-19

Ribosomal RNA (rRNA) is a central regulator of cell growth and may control cancer development. A cis noncoding rRNA (nc-rRNA) upstream from the 45S rRNA transcription start site has recently been implicated in control of rRNA transcription in mouse fibroblasts. We investigated whether a similar nc-rRNA might be expressed in human cancer epithelial cells, and related to any genomic characteristics. Using quantitative rRNA measurement, we demonstrated that a nc-rRNA is transcribed in human lung epithelial and lung cancer cells, starting from approximately -1000 nucleotides upstream of the rRNA transcription start site (+1) and extending at least to +203. This nc-rRNA was significantly more abundant in the majority of lung cancer cell lines, relative to a nontransformed lung epithelial cell line. Its abundance correlated negatively with total 45S rRNA in 12 of 13 cell lines (P = 0.014). During sequence analysis from -388 to +306, we observed diverse, frequent intercopy single nucleotide polymorphisms (SNPs) in rRNA, with a frequency greater than predicted by chance at 12 sites. A SNP at +139 (U/C) in the 5' leader sequence varied among the cell lines and correlated negatively with level of the nc-rRNA (P = 0.014). Modelling of the secondary structure of the rRNA 5'-leader sequence indicated a small increase in structural stability due to the +139 U/C SNP and a minor shift in local configuration occurrences. The results demonstrate occurrence of a sense nc-rRNA in human lung epithelial and cancer cells, and imply a role in regulation of the rRNA gene, which may be affected by a +139 SNP in the 5' leader sequence of the primary rRNA transcript.

Characterization of 16S rRNA Processing with Pre-30S Subunit Assembly Intermediates from E. coli.

PubMed

Smith, Brian A; Gupta, Neha; Denny, Kevin; Culver, Gloria M

2018-06-08

Ribosomal RNA (rRNA) is a major component of ribosomes and is fundamental to the process of translation. In bacteria, 16S rRNA is a component of the small ribosomal subunit and plays a critical role in mRNA decoding. rRNA maturation entails the removal of intervening spacer sequences contained within the pre-rRNA transcript by nucleolytic enzymes. Enzymatic activities involved in maturation of the 5'-end of 16S rRNA have been identified, but those involved in 3'-end maturation of 16S rRNA are more enigmatic. Here, we investigate molecular details of 16S rRNA maturation using purified in vivo-formed small subunit (SSU) assembly intermediates (pre-SSUs) from wild-type Escherichia coli that contain precursor 16S rRNA (17S rRNA). Upon incubation of pre-SSUs with E. coli S100 cell extracts or purified enzymes implicated in 16S rRNA processing, the 17S rRNA is processed into additional intermediates and mature 16S rRNA. These results illustrate that exonucleases RNase R, RNase II, PNPase, and RNase PH can process the 3'-end of pre-SSUs in vitro. However, the endonuclease YbeY did not exhibit nucleolytic activity with pre-SSUs under these conditions. Furthermore, these data demonstrate that multiple pathways facilitate 16S rRNA maturation with pre-SSUs in vitro, with the dominant pathways entailing complete processing of the 5'-end of 17S rRNA prior to 3'-end maturation or partial processing of the 5'-end with concomitant processing of the 3'-end. These results reveal the multifaceted nature of SSU biogenesis and suggest that E. coli may be able to escape inactivation of any one enzyme by using an existing complementary pathway. Copyright © 2018 Elsevier Ltd. All rights reserved.

Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov.

PubMed

Iino, Takao; Ohkuma, Moriya; Kamagata, Yoichi; Amachi, Seigo

2016-12-01

A chemo-organotrophic iodide (I-)-oxidizing bacterial strain, C-3T, isolated from natural gas brine of an iodine recovery facility in Kujukuri, Chiba, Japan, was characterized for representation of a novel species in the class Alphaproteobacteria. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the nearest neighbours of strain C-3T were members of the genera Eilatimonas, Kordiimonas, Rhodothalassium and Temperatibacter with 88-91 % sequence similarity. Cells of strain C-3T were aerobic, Gram-staining-negative, non-sporulating and rod-shaped (1.3-3.6 µm in length). Strain C-3T grew optimally at 30 °C, pH 7.5 and with 3 % NaCl (w/v). Iodide oxidation to form molecular iodine (I2) was a unique trait for strain C-3T, whereas the strain did not utilize iodide as a sole electron donor for chemolithoautotrophic growth. The major isoprenoid quinone was Q-10. The major cellular fatty acids were C18 : 1ω7c and C16 : 1ω5c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The G+C content of the genomic DNA was 58.5 mol%. Iodide oxidation and the major cellular fatty acids composition distinguished strain C-3T from phylogenetically related bacteria. On the basis of the phenotypic features and the phylogenetic position, a novel genus and species are proposed for strain C-3T (=JCM 17843T=LMG 28660T), to be named Iodidimonas muriae gen. nov., sp. nov. We also propose to place the distinct sublineages of the genera Iodidimonasgen. nov. and Emcibacter in the orders Iodidimonadales ord. nov. and Emcibacterales ord. nov., respectively, because these genera are located far apart from the order Kordiimonadales and form the distinct lineage in the class Alphaproteobacteria.

Comparison of Human Induced Pluripotent Stem Cell-Derived Neurons and Rat Primary CorticalNeurons as In Vitro Models of Neurite Outgrowth

EPA Science Inventory

High-throughput assays that can quantify chemical-induced changes at the cellular and molecular level have been recommended for use in chemical safety assessment. High-throughput, high content imaging assays for the key cellular events of neurodevelopment have been proposed to ra...

Relation of murine thoracic aortic structural and cellular changes with aging to passive and active mechanical properties.

PubMed

Wheeler, Jason B; Mukherjee, Rupak; Stroud, Robert E; Jones, Jeffrey A; Ikonomidis, John S

2015-02-25

Maintenance of the structure and mechanical properties of the thoracic aorta contributes to aortic function and is dependent on the composition of the extracellular matrix and the cellular content within the aortic wall. Age-related alterations in the aorta include changes in cellular content and composition of the extracellular matrix; however, the precise roles of these age-related changes in altering aortic mechanical function are not well understood. Thoracic aortic rings from the descending segment were harvested from C57BL/6 mice aged 6 and 21 months. Thoracic aortic diameter and wall thickness were higher in the old mice. Cellular density was reduced in the medial layer of aortas from the old mice; concomitantly, collagen content was higher in old mice, but elastin content was similar between young and old mice. Stress relaxation, an index of compliance, was reduced in aortas from old mice and correlated with collagen fraction. Contractility of the aortic rings following potassium stimulation was reduced in old versus young mice. Furthermore, collagen gel contraction by aortic smooth muscle cells was reduced with age. These results demonstrate that numerous age-related structural changes occurred in the thoracic aorta and were related to alterations in mechanical properties. Aortic contractility decreased with age, likely because of a reduction in medial cell number in addition to a smooth muscle contractile deficit. Together, these unique findings provide evidence that the age-related changes in structure and mechanical function coalesce to provide an aortic substrate that may be predisposed to aortopathies. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Chromobacterium haemolyticum sp. nov., a strongly haemolytic species.

PubMed

Han, Xiang Y; Han, Faye S; Segal, Jonathan

2008-06-01

A Gram-negative bacterium, strain MDA0585(T), isolated from a sputum culture, was characterized by a polyphasic approach. The 16S rRNA gene and a conserved portion of the DNA gyrase A gene were sequenced and analysed phylogenetically. Strain MDA0585(T) showed the closest relationships with Chromobacterium violaceum ATCC 12472(T) and Chromobacterium subtsugae PRAA4-1(T) (96.1 % and 96.3 % 16S rRNA gene sequence similarity, respectively). The cellular fatty acids of strain MDA0585(T) consisted mainly of C(16 : 0), C(16 : 1)omega7c and C(16 : 1)omega6c (summed feature 3) and C(18 : 1)omega7c and C(18 : 1)omega6c (summed feature 8), a profile that was similar to, but distinguishable from, those of C. violaceum ATCC 12472(T) and C. subtsugae PRAA4-1(T). In culture, strain MDA0585(T) differed from C. violaceum and C. subtsugae in several ways: lack of violet pigmentation, the ability to haemolyse sheep blood, differences in several biochemical reactions and higher resistance to antibiotics. The culture supernatant of strain MDA0585(T) also caused remarkable haemolysis of human erythrocytes. These results suggest that strain MDA0585(T) represents a novel species within the genus Chromobacterium, for which the name Chromobacterium haemolyticum sp. nov. is proposed. The type strain is MDA0585(T) (=CCUG 53230(T)=JCM 14163(T)=DSM 19808(T)).

The Primary open-angle glaucoma gene WDR36 functions in ribosomal RNA processing and interacts with the p53 stress–response pathway

PubMed Central

Skarie, Jonathan M.; Link, Brian A.

2008-01-01

Primary open-angle glaucoma (POAG) is a genetically complex neuropathy that affects retinal ganglion cells and is a leading cause of blindness worldwide. WDR36, a gene of unknown function, was recently identified as causative for POAG at locus GLC1G. Subsequent studies found disease-associated variants in control populations, leaving the role of WDR36 in this disease unclear. To address this issue, we determined the function of WDR36. We studied Wdr36 in zebrafish and found it is the functional homolog of yeast Utp21. Utp21 is cell essential and functions in the nucleolar processing of 18S rRNA, which is required for ribosome biogenesis. Evidence for functional homology comes from sequence alignment, ubiquitous expression, sub-cellular localization to the nucleolus and loss-of-function phenotypes that include defects in 18S rRNA processing and abnormal nucleolar morphology. Additionally, we show that loss of Wdr36 function leads to an activation of the p53 stress–response pathway, suggesting that co-inheritance of defects in p53 pathway genes may influence the impact of WDR36 variants on POAG. Although these results overall do not provide evidence for or against a role of WDR36 in POAG, they do provide important baseline information for future studies. PMID:18469340

Changes in the community structure of free-living heterotrophic bacteria in the open tropical Pacific Ocean in response to microalgal lysate-derived dissolved organic matter.

PubMed

Tada, Yuya; Suzuki, Koji

2016-07-01

Dissolved organic matter derived from phytoplankton (DOMP) can affect the bacterial biomass and community structure in aquatic ecosystems. Here, we examined the community response of free-living heterotrophic bacteria, with respect to cellular nucleic acid levels, to the DOMP lysates derived from three phytoplankton strains in the open tropical Pacific. The free amino acid (FAA) composition of each DOMP lysate differed among the microalgal strains. Terminal restriction fragment-length polymorphism analyses with 16S rRNA genes revealed that the community shifts of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria varied significantly with the different DOMP lysate treatments. Furthermore, the FAA composition in DOMP lysates significantly affected the bacterial community shifts in HNA and LNA. Similarity percentage analysis using 16S rRNA gene deep-sequencing revealed that the DOMP lysates from the pelagophyte Pelagomonas calceolata caused relatively large community shifts with Alcaligenes predominating in the HNA fraction. In contrast, the DOMP lysate from the diatom Thalassiosira oceanica induced a community shift in the LNA fraction with a predominance of uncultured Actinobacteria Thus, the data indicate that the DOMP lysates from different microalgae constitute a primary factor altering the dominant bacterial groups in the open ocean. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Proposal of Mucilaginibacter galii sp. nov. isolated from leaves of Galium album.

PubMed

Aydogan, Ebru L; Busse, Hans-Jürgen; Moser, Gerald; Müller, Christoph; Kämpfer, Peter; Glaeser, Stefanie P

2017-05-01

A pale-pink-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterial strain, PP-F2F-G47T, was isolated from the phyllosphere of the herbaceous plant Galium album. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence revealed highest sequence similarity to the type strains of Mucilaginibacter daejeonensis (96.2 %), Mucilaginibacter dorajii (95.7 %) and Mucilaginibacter phyllosphaerae (95.5 %). 16S rRNA gene sequence similarities to all other type strains were below 95.5 %. The predominant cellular fatty acids of the strain were C16 : 1ω7c/iso-C15 : 0 2-OH (measured as summed feature 3) and iso-C15 : 0. The major compound in the polyamine pattern was sym-homospermidine and major quinone was menaquinone MK-7. The polar lipid profile was composed of phosphatidylethanolamine and several unidentified aminolipipids, phospholipids, aminophospholipids and lipids without a functional group. A sphingophospholipid could not be detected but a ninhydrin-positive alkaline-stable lipid was visible. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses a novel species is proposed, Mucilaginibacter galii sp. nov., with PP-F2F-G47T (=CCM 8711T=CIP 111182T=LMG 29767T) as the type strain.

Cellular therapy injections in today's orthopedic market: A social media analysis.

PubMed

Ramkumar, Prem N; Navarro, Sergio M; Haeberle, Heather S; Chughtai, Morad; Demetriades, Christopher; Piuzzi, Nicolas S; Mont, Michael A; Bauer, Thomas W; Muschler, George F

2017-12-01

The current state of cellular therapy for musculoskeletal conditions is at a crossroads. Marketing efforts are often outpacing clinical evidence and regulatory control. This study was an effort to describe the marketing of cellular therapy in musculoskeletal medicine by evaluating the content in popular social media channels. Specifically, media posts were evaluated for the following: (1) perspective, (2) tone, (3) content and (4) visibility. Social media content related to cell therapy for musculoskeletal conditions was assessed in a search using 28 hashtags on the public domains of Instagram and Twitter over a 2-year period (2014-2016) that resulted in analysis of 698 posts. Supplemental analyses of LinkedIn and Facebook domains were also conducted. A categorical scoring system was used to analyze perspective (patient, family or friend, business or organization), tone (positive, negative), content (education, advertisement, research, media coverage or patient experience) and visibility (number of hashtags per post). Sub-analyses of the advertisement content from various perspectives (patients, physicians and businesses) were performed. The media perspective was most frequently from a business or organization (83%; n = 575). A total of 94% of the posts had a positive tone and only 6% had a negative tone, and the only negative posts came from patients (60% positive and 40% negative). The most common content of social media posts were advertisements, representing 68% (n = 477) of all posts; this was confirmed in the Facebook analysis. The mean number of hashtags was five per post. Sub-analyses revealed approximately half of the advertising posts originated from a single business that recruited physicians to market their cell-based therapies on social media, which was confirmed in the LinkedIn analysis. The market messages related to cell-based therapies for musculoskeletal conditions available on social media are dominated by businesses that seem to use a network of physicians, apply several hashtags to enhance visibility and advertise these largely unproven modalities. The posts portray an almost exclusively positive tone, without providing a "fair balance" on the risks, benefits and limitations. Copyright © 2017 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Evolutionary tradeoffs in cellular composition across diverse bacteria

PubMed Central

Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

2016-01-01

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage.

PubMed

Kobayashi, Hisami; Nakasato, Takuya; Sakamoto, Mitsuo; Ohtani, Yoshihisa; Terada, Fuminori; Sakai, Ken; Ohkuma, Moriya; Tohno, Masanori

2017-12-01

A Gram-stain-variable, strictly anaerobic, rod-shaped, catalase-negative and endospore-forming bacterial strain, designated MJC39 T , was isolated from grass silage preserved in Hokkaido, Japan. Growth occurred at 20-42 °C, pH 5.0-7.0 and NaCl concentrations up to 2 % (w/v). The isolated strain MJC39 T produced butyric acid in peptone yeast extract medium with glucose. The DNA G+C content of strain MJC39 T was 34.4±0.2 mol%. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and summed feature 3 (including C16 : 1ω7c/C16 : 1ω6c). No respiratory quinones were detected. The polar lipids of strain MJC39 T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified lipid, one unidentified aminolipid, two unidentified glycolipids, one unidentified phospholipid, one unidentified aminoglycolipid and one unidentified phosphoaminoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJC39 T was a member of the genus Clostridium and is closely related to Clostridium tyrobutyricum JCM 11008 T (95.8 % similarity) and Clostridium algifaecis MB9-7 T (95.5 % similarity). Based on the genotypic, phenotypic and chemotaxonomic characteristics, strain MJC39 T represents a novel species of the genus Clostridium, for which the name Clostridium pabulibutyricum sp. nov. is proposed. The type strain is MJC39 T (=JCM 31506 T =DSM 103944 T ).

Devosia honganensis sp. nov., isolated from the soil of a chemical factory.

PubMed

Zhang, Long; Song, Man; Chen, Xiao-Long; Xu, Ren-Jie; Chen, Kai; Li, Shun-Peng; Xia, Zhen-Yuan; Jiang, Jian-Dong

2015-12-01

A Gram-negative, strictly aerobic, yellow-pigmented and rod-shaped bacterium, designated strain NSL10(T), was isolated from the waste surface soil of a chemical factory in Hongan, China. Strain NSL10(T) was found to grow optimally at pH 7.0, 30 °C and in the absence of NaCl in modified LB medium. Cells were found to be positive for catalase and oxidase. The G+C content of the total DNA was determined to be 66.8 mol%. The 16S rRNA gene sequence of strain NSL10(T) showed the highest similarity to that of Devosia albogilva IPL15(T) (96.80 %), followed by Devosia geojensis BD-c194(T) (96.46 %) and Devosia chinhatensis IPL18(T) (96.27 %). The major cellular fatty acids of strain NSL10(T) were identified as C18:1 ω7c/C18:1 ω6c (48.2 %) and C16:0 (17.7 %). The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and an unidentified compound. Minor amounts of unidentified glycolipids and unidentified polar lipids were also detected. These chemotaxonomic data supported the affiliation of strain NSL10(T) to the genus Devosia. In conclusion, on the basis of biochemical, physiological characteristics and molecular properties, strain NSL10(T) represents a novel species within the genus Devosia, for which the name Devosia honganensis sp. nov., is proposed. The type strain is NSL10(T) (=KCTC 42281(T) = ACCC 19737(T)).

Spirosoma jeollabukense sp. nov., isolated from soil.

PubMed

Li, Weilan; Ten, Leonid N; Lee, Seung-Yeol; Lee, Dong Hoon; Jung, Hee-Young

2018-04-01

A Gram-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S2-3-6 T , was isolated from soil in Jeollabuk-do province, South Korea, and was characterized taxonomically using a polyphasic approach. According to a comparative 16S rRNA gene sequence analysis, strain S2-3-6 T belonged to the family Cytophagaceae and was most closely related to Spirosoma endophyticum EX36 T (98.2%), Spirosoma fluviale MSd3 T (96.0%), and Spirosoma linguale DSM 74 T (95.7%). Strain S2-3-6 T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and C16:0 N alcohol as major cellular fatty acids, MK-7 as the predominant respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain S2-3-6 T was 47.8%. Phenotypic and chemotaxonomic data supported the affiliation of strain S2-3-6 T to the genus Spirosoma. However, the DNA-DNA relatedness between strain S2-3-6 T and Spirosoma endophyticum KACC 17920 T was 27%, clearly showing that the isolate constitutes a new genospecies. Strain S2-3-6 T could be clearly differentiated from its closest neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, strain S2-3-6 T represents a novel species of the genus Spirosoma, for which the name Spirosoma jeollabukense sp. nov. is proposed. The type strain is S2-3-6 T (= KCTC 52725 T  = JCM 32129 T ).

Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malik, Afshan N., E-mail: afshan.malik@kcl.ac.uk; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana

2011-08-19

Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that themore » methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.« less

Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis.

PubMed

Finegold, Sydney M; Vaisanen, Marja-Liisa; Rautio, Merja; Eerola, Erkki; Summanen, Paula; Molitoris, Denise; Song, Yuli; Liu, Chengxu; Jousimies-Somer, Hannele

2004-11-01

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of alpha-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and was designated a P. endodontalis-like organism for some time. However, P. endodontalis is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore, P. uenonis is glycerol positive in the Biolog AN Microplate system. Both P. asaccharolytica and P. uenonis are positive by 13 other tests in the Biolog system, whereas P. endodontalis is negative by all of these tests. P. asaccharolytica grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and P. endodontalis but less than 2% sequence difference between the novel species and P. asaccharolytica. Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from P. asaccharolytica. We propose the name Porphyromonas uenonis for the novel species. We have recovered P. uenonis from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children.

Porphyromonas uenonis sp. nov., a Pathogen for Humans Distinct from P. asaccharolytica and P. endodontalis

PubMed Central

Finegold, Sydney M.; Vaisanen, Marja-Liisa; Rautio, Merja; Eerola, Erkki; Summanen, Paula; Molitoris, Denise; Song, Yuli; Liu, Chengxu; Jousimies-Somer, Hannele

2004-01-01

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of α-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and was designated a P. endodontalis-like organism for some time. However, P. endodontalis is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore, P. uenonis is glycerol positive in the Biolog AN Microplate system. Both P. asaccharolytica and P. uenonis are positive by 13 other tests in the Biolog system, whereas P. endodontalis is negative by all of these tests. P. asaccharolytica grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and P. endodontalis but less than 2% sequence difference between the novel species and P. asaccharolytica. Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from P. asaccharolytica. We propose the name Porphyromonas uenonis for the novel species. We have recovered P. uenonis from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children. PMID:15528728

Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.

PubMed

Muramatsu, Yuki; Kamakura, Yuki; Takahashi, Mai; Nakagawa, Yasuyoshi

2017-06-01

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes. Levels of DNA-DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and β-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga, named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

Oceanobacillus damuensis sp. nov. and Oceanobacillus rekensis sp. nov., isolated from saline alkali soil samples.

PubMed

Long, Xiufeng; Ye, Renyuan; Zhang, Shuai; Liu, Bo; Zhang, Yuqin; Zeng, Zhigang; Tian, Yongqiang

2015-09-01

Two moderately halophilic strains, PT-11(T) and PT-20(T), were isolated from saline alkali soil samples collected in Shache County, Xinjiang Province, China. Both strains are aerobic, Gram-positive, motile rods. Strain PT-11(T) grows at 15-40 °C and at pH 6.5-10.0, while PT-20(T) grows at 15-40 °C and at pH 6.5-11.0. The major cellular fatty acids in both strains include anteiso-C15:0, anteiso-C17:0 and iso-C15:0. For both strains, the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and several unidentified lipids. In addition, strain PT-20(T) also contains phosphatidylcholine. The major isoprenoid quinone for both strains is MK-7. The genomic G+C content is 36.7 % for PT-11(T) and 39.2 % for PT-20(T). Phylogenetic analyses of 16S rRNA gene sequences indicated that these two isolates are members of the genus Oceanobacillus. DNA-DNA hybridization indicated that strains PT-11(T) and PT-20(T) should be considered two distinct species. On the basis of both phylogenetic and chemotaxonomic data analyses, therefore, we conclude that PT-11(T) and PT-20(T) represent two novel species within the genus Oceanobacillus, for which we propose the names Oceanobacillus rekensis sp. nov. and Oceanobacillus damuensis sp. nov., respectively. The type strains are PT-11(T) (=KCTC 33144(T) = DSM 26900(T)) and PT-20(T) (=KCTC 33146(T) = DSM 26901(T)).

Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.

PubMed

Lee, Do-Hoon; Cha, Chang-Jun

2017-11-01

A novel bacterial strain, designated CJ661 T , was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661 T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661 T grew optimally at 30 °C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661 T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276 T (98.1 %), followed by Ramlibacter henchirensis DSM 14656 T (97.1 %). DNA-DNA relatedness levels of strain CJ661 T were 40.6 % to R. ginsenosidimutans KCTC 22276 T and 25.0 % to R. henchirensis DSM 14656 T . The major isoprenoid quinone was ubiquinone (Q-8). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain CJ661 T were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The G+C content of the genomic DNA was 65.4 mol%. On the basis polyphasic taxonomic data, strain CJ661 T represents a novel species in the genus Ramlibacter, for which name Ramlibacter alkalitolerans sp. nov. is proposed; the type strain is CJ661 T (=KACC 19305 T =JCM 32081 T ).

Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.

PubMed

Kim, Yoon-Gon; Jin, Yeon-A; Hwang, Chung Yeon; Cho, Byung Cheol

2008-01-01

A Gram-negative, strictly aerobic, marine bacterium, designated strain CL-YJ9(T), was isolated from sediment closely associated with the roots of a plant (Suaeda japonica) inhabiting a coastal tidal flat. Cells of the novel strain were straight and rod-shaped and were motile by means of monopolar flagella. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CL-YJ9(T) belongs to the genus Marinobacterium and was most closely related to Marinobacterium halophilum mano11(T) (94.1% sequence similarity) and to other members of the genus Marinobacterium (92.5-93.7% sequence similarity). The strain grew with 1-5% NaCl (optimum, 3%) and at 5-30 degrees C (optimum, approx. 25 degrees C) and pH 6.0-9.0 (optimum, pH 7.0). The predominant cellular fatty acids were summed feature 3 (C(16:1)omega7c and/or iso-C(15:0) 2-OH, 40.3%), C(18:1)omega7c (26.6%), C(16:0) (16.6%) and C(10:0) 3-OH (7.1%). The major isoprenoid quinone was Q-8. The G+C content of the genomic DNA was 61 mol%. On the basis of the data from this polyphasic study, strain CL-YJ9(T) belongs to the genus Marinobacterium but is distinguishable from the recognized species. Strain CL-YJ9(T) therefore represents a novel species, for which the name Marinobacterium rhizophilum sp. nov. is proposed. The type strain is CL-YJ9(T) (=KCCM 42386(T) =DSM 18822(T)).

Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand.

PubMed

Namwong, Sirilak; Tanasupawat, Somboon; Smitinont, Thitapha; Visessanguan, Wonnop; Kudo, Takuji; Itoh, Takashi

2005-01-01

Eight strains of aerobic, spore-forming, Gram-positive, moderately halophilic bacteria were isolated from sauce (nam-pla and bu-du) produced in Thailand by the fermentation of fish. They grew optimally in the presence of 10 % NaCl, at 37 degrees C and pH 7.0. A diagnostic diamino acid, meso-diaminopimelic acid, was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(16 : 0). Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were found to be the major polar lipid components. The DNA G+C content was 42-43 mol%. These bacteria were further divided into two groups based on phenotypic characteristics and DNA-DNA similarities. Three strains of Group I were highly affiliated to the type strain of Lentibacillus salicampi in terms of phenotypic characterization and DNA-DNA similarities (96-102 %); accordingly, they were identified as strains of L. salicampi. A representative strain of Group II, strain IS40-3T, was most closely related to L. salicampi in terms of 16S rRNA-based phylogenetic analysis, although five strains of Group II could be distinguished from L. salicampi by means of several phenotypic properties, low 16S rRNA gene sequence similarity (95.2 %) and low DNA-DNA similarities (12-32 %). Therefore, the Group II strains should be included in a novel species of the genus Lentibacillus, for which the name Lentibacillus juripiscarius sp. nov. is proposed. The type strain is IS40-3T (=JCM 12147T=PCU 229T=TISTR 1535T).

Spirosoma flavum sp. nov., isolated from Arctic tundra soil.

PubMed

Zou, Rui; Zhang, Yumin; Zhou, Xueyin; Wang, Yang; Peng, Fang

2017-12-01

A yellow-pigmented strain, designated Y4AR-5 T , was characterized by using a polyphasic approach. The strain was isolated from a tundra soil from near Longyearbyen, Svalbard Islands, Norway. The cells were Gram-stain-negative, aerobic, rod-shaped and non-motile. Growth occurred at 4-28 °C (optimum 20 °C) and pH 6.0-9.0 (optimum pH 8.0) and with 0-0.5 % (w/v) NaCl (optimum 0 %). The major respiratory quinone was MK-7. The polar lipids were phosphatidylethanolamine (PE), an aminophospholipid (APL), a phospholipid (PL), an unidentified aminolipid (AL) and two unidentified lipids. The results of analysis of the 16S rRNA gene indicated that the novel strain was most closely related to members of the genus Spirosoma (96.2 % sequence similarity with Spirosoma endophyticum). The genomic DNA G+C content was 45.9 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain Y4AR-5 T should be classified as representing a novel species of the genus Spirosoma, for which the name Spirosomaflavum sp. nov. is proposed. The type strain is Y4AR-5 T (=CCTCC AB 2015352 T =KCTC 52490 T ).

Serratia oryzae sp. nov., isolated from rice stems.

PubMed

Zhang, Cai-Wen; Zhang, Jun; Zhao, Juan-Juan; Zhao, Xia; Zhao, Dong-Fang; Yin, Hua-Qun; Zhang, Xiao-Xia

2017-08-01

A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia. The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA-DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia. Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia, for which the name Serratia oryzae sp. nov. is proposed.

Flavisolibacter carri sp. nov., isolated from an automotive air-conditioning system.

PubMed

Lee, Hyosun; Kim, Dong-Uk; Lee, Suyeon; Kim, Song-Gun; Park, A-Young; Ahn, Jae-Hyung; Ka, Jong-Ok

2018-04-18

A Gram-stain negative, aerobic, non-motile, rod-shaped and yellow bacterium, designated TX0651 T , was isolated from an automotive air-conditioning system. Phylogenetically, the strain groups with the members of the genus Flavisolibacter and exhibits high 16S rRNA gene sequence similarities with Flavisolibacter ginsenosidimutans Gsoil 636 T (97.4%), Flavisolibacter ginsengiterrae Gsoil 492 T (96.3%) and Flavisolibacter ginsengisoli Gsoil 643 T (96.2%). DNA-DNA relatedness between TX0651 T and F. ginsenosidimutans KCTC 22818 T and F. ginsengiterrae KCTC 12656 T were determined to be less than 40%. The low levels of DNA-DNA relatedness identifies the strain TX0651 T as a novel species in the genus Flavisolibacter. The major cellular fatty acids were identified as iso-C 15:0 , summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c), iso-C 15:1 G and iso-C 17:0 3-OH. The predominant respiratory quinone was identified as MK-7. The polar lipids were found to be comprised of phosphatidylethanolamine, unidentified amino-glycophospholipids, an unidentified aminophospholipid, an unidentified amino lipid and unidentified lipids. The DNA G+C content of the strain was determined to be 31.2 mol%. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain TX0651 T should be classified in a novel species in the genus Flavisolibacter, for which the name Flavisolibacter carri sp. nov. (= KACC 19014 T  = KCTC 52836 T  = NBRC 111784 T ) is proposed.

Deinococcus petrolearius sp. nov. isolated from crude oil recovery water in China.

PubMed

Xi, Lijun; Qiao, Nenghu; Zhang, Jingjing; Li, Jing; Liu, Dejian; You, Jing; Liu, Jianguo

2018-03-01

A Gram-stain positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain 6.1 T , was isolated from a crude oil recovery water sample from the Huabei oil field in China. The novel strain exhibited tolerance of UV irradiation (> 1000 J m -2 ). Based on 16S rRNA gene sequence comparisons, strain 6.1 T shows high similarity to Deinococcus citri DSM 24791 T (98.1%) and Deinococcus gobiensis I-0 T (97.8%), with less than 93.5% similarity to other closely related taxa. The major cellular fatty acids were identified as summed feature 3 (C 16:1 ω7c and/or iso-C 15:0 2-OH), followed by iso-C 17:1 ω9c and C 16:0 . The polar lipid profile was found to contain phospholipids, glycolipids, phosphoglycolipids and aminophospholipids. The predominant respiratory quinone was identified as MK-8. The DNA G + C content was determined to be 68.3 mol %. DNA-DNA hybridization between strain 6.1 T and D. citri DSM 24791 T was 45.6 ± 7.1% and with D. gobiensis I-O T was 36.6 ± 4.7%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, we conclude strain 6.1 T represents a novel species of the genus Deinococcus, for which we propose the name Deinococcus petrolearius sp. nov. The type strain is 6.1 T (= CGMCC 1.15053 T  = KCTC 33744 T ).

Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond.

PubMed

Zhang, Heng-Xi; Zhao, Jin-Xin; Chen, Guan-Jun; Du, Zong-Jun

2016-05-01

A marine bacterium, designated strain N39(T), was isolated from a sediment sample collected at a sea cucumber culture pond in Weihai, China. Cells of strain N39(T) were observed to be Gram-stain negative, facultatively anaerobic, motile rods showing catalase and oxidase negative reactions. Strain N39(T) was found to grow optimally at pH 8.0-8.5, 35-37 °C and in the presence of approximately 3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N39(T) belongs to the genus Kordiimonas in the family Kordiimonadaceae, appearing closely related to Kordiimonas lacus JCM 16261(T) (95.9 %), Kordiimonas aquimaris MEBiC06554(T) (95.1 %), Kordiimonas gwangyangensis JCM 12864(T) (94.2 %) and Kordiimonas aestuarii 101-1(T) (93.8 %). Ubiquinone 10 (Q-10) was found to be the major respiratory quinone. The dominant cellular fatty acids were identified as iso-C17:1 ω9c, iso-C17:0, iso-C15:0 and C17:1 ω6c. The predominant polar lipids were found to be phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. The DNA G + C content of strain N39(T) is 50.8 %. On the basis of genotypic, chemotaxonomic and phenotypic data, strain N39(T) is concluded to represent a novel species within the genus Kordiimonas, for which the name Kordiimonas sediminis sp. nov. is proposed. The type strain is N39(T) (=KCTC 42590(T) = MCCC 1H00112(T)).

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

PubMed

Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

2014-06-01

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). © 2014 IUMS.

Umboniibacter roseus sp. nov., isolated from coastal seawater.

PubMed

Sung, Hye-Ri; Kim, Mibang; Shin, Kee-Sun

2015-11-01

A Gram-reaction-negative, non-motile, strictly aerobic, dark pink-pigmented and rod-shaped bacterial isolate, designated 14-121-B13T, was isolated from surface seawater off the coast of the South Sea at Namhae-gun, Republic of Korea. Cells were catalase- and oxidase-positive and required NaCl for growth. Strain 14-121-B13T grew optimally at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7.5-8.0.Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain 14-121-B13T clustered with the type strain of Umboniibacter marinipuniceus, with which it exhibited 96.7 % sequence similarity. The DNA G+C content of strain 14-121-B13T was 48.9 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major respiratory quinone was ubiquinone Q-7 and the polar lipids detected in strain 14-121-B13T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, unidentified phospholipids, unidentified aminophospholipids and unidentified lipids. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain 14-121-B13T is considered to represent a novel species of the genus, Umboniibacter for which the name Umboniibacter roseus sp. nov. is proposed. The type strain is 14-121-B13T ( = DSM 29882T = KCTC 42467T).

Molecular and cellular neurocardiology: development, and cellular and molecular adaptations to heart disease

PubMed Central

Anderson, Mark E.; Birren, Susan J.; Fukuda, Keiichi; Herring, Neil; Hoover, Donald B.; Kanazawa, Hideaki; Paterson, David J.; Ripplinger, Crystal M.

2016-01-01

Abstract The nervous system and cardiovascular system develop in concert and are functionally interconnected in both health and disease. This white paper focuses on the cellular and molecular mechanisms that underlie neural–cardiac interactions during development, during normal physiological function in the mature system, and during pathological remodelling in cardiovascular disease. The content on each subject was contributed by experts, and we hope that this will provide a useful resource for newcomers to neurocardiology as well as aficionados. PMID:27060296

The Use of a Sensory Model to Facilitate the Study of the Biochemistry of Adhesion in Marine-Fouling Diatoms

DTIC Science & Technology

1993-07-30

transported to the cell membrane in the area of the raphe canal and, following vesicular fusion with the cellular membrane, their contents are released into...the external raphe canal and become free to interact with the substratum. This leads to cellular adhesion. Continued synthesis and secretion of polymer... cellular adhesion is measured as a function of an extracellular chemical signal. Results (a) Sensory Biology. The overall question in our research

The complete mitochondrial genome of the longhorn beetle Xylotrechus grayii (Coleoptera: Cerambycidae).

PubMed

Guo, Kun; Chen, Jun; Xu, Chang-Qing; Qiao, Hai-Li; Xu, Rong; Zhao, Xiang-Jian

2016-05-01

We sequenced the complete mitochondrial genome of the longhorn beetle, Xylotrechus grayii. The total length of the X. grayii mitogenome was 15,540 bp with an A + T content of 75.29%, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and an A + T-rich region. All the genes were arranged in the same order as that of the ancestral insect. All PCGs started with a typical ATN codon except for cox1 and nad1, which used TTG as start codon. Ten out of 13 PCGs terminated with incomplete codons (TA or T). The A + T-rich region was 893 bp in length with an A + T content of 85.89 %.

Biochemical changes to fibroblast cells subjected to ionizing radiation.

PubMed

Jones, Pamala; Benghuzzi, Hamed; Tucci, Michelle; Richards, Latoya; Harrison, George; Patel, Ramesh

2008-01-01

High energy X-rays are capable of interacting with biological membranes to cause both functional and structural modifications. The goal of the present study was to investigate the effects human fibroblast cells exposed multiple times to 10 Gy over time. Following exposures of 2, 3, or 4 times to 10 Gy/10min the cells were evaluated for cell number changes, membrane damage, and intracellular glutathione content after 24, 48 and 72 hours. Twenty-four hours following exposure the cell numbers were reduced and increased levels of cellular membrane damage was evident. This trend was observed for the duration of the study. Interestingly, there was not an exposure dependent increase in cell damage or cell loss with time. Intracellular antioxidant systems were activated as indicated by anincrease in total cellular glutathione content. Additional studies are needed to determine if the cellular reduction is caused by a direct effect of the X-rays targeting the DNA or an indirect effect of the X-ray targeting the cellular membrane, which then generates radicals that target cell cycle checkpoints or DNA damage. In conclusion, fibroblast cells can be used to determine early and late events of cellular function following exposure to harmful levels of radiation exposure and results of exposure can be seen within twenty four hours.

Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.

PubMed

Kim, Soo-Jin; Lim, Jun-Muk; Ahn, Jae-Hyung; Weon, Hang-Yeon; Hamada, Moriyuki; Suzuki, Ken-ichiro; Ahn, Tae-Young; Kwon, Soon-Wo

2014-02-01

Bacterial strains KIS82-1(T) and GRS42(T) were isolated from soil and from sap of Acer mono, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS82-1(T) showed the highest similarity to those of Frondihabitans peucedani RS-15(T) (97.6%), Frigoribacterium mesophilum MSL-08(T) (97.2%) and Labedella gwakjiensis KSW2-17(T) (97.0%), while strain GRS42(T) showed the highest 16S rRNA gene sequence similarity to Frondihabitans peucedani RS-15(T) (98.7%), Frondihabitans cladoniiphilus CafT13(T) (98.4%), Frondihabitans australicus E1HC-02(T) (98.2%) and Frigoribacterium faeni 801(T) (97.3%). The 16S rRNA gene sequence similarity between GRS42(T) and KIS82-1(T) was 97.0%. Phylogenetic trees indicated that strain GRS42(T) was firmly grouped into the genus Frondihabitans, while strain KIS82-1(T) did not show a clear affiliation to any genus within the family Microbacteriaceae. Strain KIS82-1(T) showed type B1β peptidoglycan with 2,4-diamino-L-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C(15 : 0), iso-C(16: 0) and iso-C(14 : 0) as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42(T) was of type B2β with D-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42(T) revealed low DNA-DNA hybridization (<50% relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1(T) represents a novel genus and species and that strain GRS42(T) represents a novel species in the family Microbacteriaceae. The genus Galbitalea gen. nov. is proposed, with strain KIS82-1(T) ( = KACC 15520(T) = NBRC 108727(T)) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42(T) ( = KACC 15521(T) = NBRC 108728(T)) is proposed as the type strain of Frondihabitans sucicola sp. nov.

[Intranuclear distribution of rat liver ribosomal RNA].

PubMed

Dabeva, M D; Todorov, B N; Khadzhiolova, A A

1976-03-01

A method is described for the isolation of pure liver nuclei with minimal cytoplasmic contaminants, loss of nuclear RNA and degradation of nuclear RNA. The RNA components are extracted in three distinct fractions by subsequent treatment with phenol at 4 degrees, 50 degrees and 85 degrees C. The total and 14C-orotate labelled RNA components in the three nuclear RNA fractions are characterized by nucleotide composition, poly(A)-RNA content and agar-gel electrophoresis. The results show that the RNA in three fractions correspond to the nucleosol, nucleolus and chromatin compartments of the nucleus. The nuclear HnRNA components are exclusively in the 85 degrees C RNA. Nuclear ribosomal RNA is extracted in the 4 degrees C and 50 degrees C RNA fractions. These two nuclear RNA fractions are distinct in constituent pre-rRNA species and the rate of labelling of their rRNA components. The amount of the pre-rRNA and rRNA species is determined. The results show that the nucleolus-nucleosol and nucleosol-cytoplasm transitions of ribosomal subparticles are markedly slower processes than the preceeding steps of ribosome biogenesis.

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

PubMed Central

Seligmann, Hervé; Raoult, Didier

2018-01-01

We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing). PMID:29449833

Frequency of bacetrial content finding in persistant periapical lesions

PubMed Central

Grgurević, Joško; Tambić Andrašević, Arjana; Prpić Mehičić, Goranka; Kuzmac, Sania; Jukić, Silvana

2017-01-01

Objectives To determine the percentage of persistant apical lesions positive for bacterial nucleic acids, to detect microorganisms difficult to cultivate in persistant apical lesions by PCR and relate them to endodontic failure, clinical symptoms and diabetes mellitus. Materials and methods The samples of persistent apical lesions were collected during apicoectomy. Bacterial ubiquitous primer 16S rRNA was used to detect 16S ribosomal RNA in 36 samples. A species–specific PCR was performed with primers targeted to the bacterial 16S rRNA genes of Prevotella Nigrescens, Pseudoramibacter alactolyticus, and Propionobacterium propionicum. Results Six samples (16.67%) were positive for bacterial ribosomal RNA. Pseudoramibacter alactolyticus was detected in three samples. Propionibacterium propionicum and Prevotella nigrescens were detected in one sample each. The prevalence of infection of such lesions with P. intermedia, P. propionicum and P. alactolyticus is low. Conslusion The study we conducted gave insufficient data about extraradicular infection and its connection with diabetes mellitus and clinical symptoms. Conclusions Apical lesions persisting after endodontic treatment could harbor microorganisms other than Actinomyces and Propionicum species. PMID:29225362

Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.

PubMed

Ren, Xiaopu; Li, Mingyang; Guo, Dongqi

2016-09-01

A Gram-strain-positive bacterial strain 48(T) was isolated from traditional yogurt in Xinjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, polymerase α subunit (rpoA) gene sequence analysis, determination of DNA G+C content, DNA-DNA hybridization with the type strain of Enterococcus ratti and analysis of phenotypic features. Strain 48(T) accounted for 96.1, 95.8, 95.8, and 95.7 % with Enterococcus faecium CGMCC 1.2136(T), Enterococcus hirae ATCC 9790(T), Enterococcus durans CECT 411(T), and E. ratti ATCC 700914(T) in the 16S rRNA gene sequence similarities, respectively. The sequence of rpoA gene showed similarities of 99.0, 96.0, 96.0, and 96 % with that of E. faecium ATCC 19434(T), Enterococcus villorum LMG12287, E. hirae ATCC 9790(T), and E. durans ATCC 19432(T), respectively. Based upon of polyphasic characterization data obtained in the study, a novel species, Enterococcus xinjiangensis sp. nov., was proposed and the type strain was 48(T)(=CCTCC AB 2014041(T) = JCM 30200(T)).

Streptococcus tangierensis sp. nov. and Streptococcus cameli sp. nov., two novel Streptococcus species isolated from raw camel milk in Morocco.

PubMed

Kadri, Zaina; Vandamme, Peter; Ouadghiri, Mouna; Cnockaert, Margo; Aerts, Maarten; Elfahime, El Mostafa; Farricha, Omar El; Swings, Jean; Amar, Mohamed

2015-02-01

Biochemical and molecular genetic studies were performed on two unidentified Gram-stain positive, catalase and oxidase negative, non-hemolytic Streptococcus-like organisms recovered from raw camel milk in Morocco. Phenotypic characterization and comparative 16S rRNA gene sequencing demonstrated that the two strains were highly different from each other and that they did not correspond to any recognized species of the genus Streptococcus. Phylogenetic analysis based on 16S rRNA gene sequences showed the unidentified organisms each formed a hitherto unknown sub-line within the genus Streptococcus, displaying a close affinity with Streptococcus moroccensis, Streptococcus minor and Streptococcus ovis. DNA G+C content determination, MALDI-TOF mass spectrometry and biochemical tests demonstrated the bacterial isolates represent two novel species. Based on the phenotypic distinctiveness of the new bacteria and molecular genetic evidence, it is proposed to classify the two strains as Streptococcus tangierensis sp. nov., with CCMM B832(T) (=LMG 27683(T)) as the type strain, and Streptococcus cameli sp. nov., with CCMM B834(T) (=LMG 27685(T)) as the type strain.

Roseomonas wooponensis sp. nov., isolated from wetland freshwater.

PubMed

Lee, Ji Hee; Kim, Mi Sun; Baik, Keun Sik; Kim, Hyang Mi; Lee, Kang Hyun; Seong, Chi Nam

2015-11-01

A non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram-stain-negative, catalase- and oxidase-positive. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0.The predominant quinone and polyamine were ubiquinone 10 (Q-10) and spermidine, respectively. The DNA G+C content was 71 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WW53T belongs to the family Acetobacteraceae, and is related to the genus Roseomonas. Strain WW53T was most closely related to Roseomonas stagni HS-69T (95.3 % 16S rRNA gene sequence similarity). Results of a polyphasic taxonomy study suggested that the isolate represents a novel species in the genus Roseomonas, for which the name Roseomonas wooponensis sp. nov. is proposed. The type strain is WW53T ( = KCTC 32534T = JCM 19527T).

The complete chloroplast genome sequence of Dendrobium officinale.

PubMed

Yang, Pei; Zhou, Hong; Qian, Jun; Xu, Haibin; Shao, Qingsong; Li, Yonghua; Yao, Hui

2016-01-01

The complete chloroplast sequence of Dendrobium officinale, an endangered and economically important traditional Chinese medicine, was reported and characterized. The genome size is 152,018 bp, with 37.5% GC content. A pair of inverted repeats (IRs) of 26,284 bp are separated by a large single-copy region (LSC, 84,944 bp) and a small single-copy region (SSC, 14,506 bp). The complete cp DNA contains 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Fourteen genes contained one or two introns.

Treatment of Articular Cartilage Defects in the Goat with Frozen Versus Fresh Osteochondral Allografts: Effects on Cartilage Stiffness, Zonal Composition, and Structure at Six Months

PubMed Central

Pallante, Andrea L.; Görtz, Simon; Chen, Albert C.; Healey, Robert M.; Chase, Derek C.; Ball, Scott T.; Amiel, David; Sah, Robert L.; Bugbee, William D.

2012-01-01

Background: Understanding the effectiveness of frozen as compared with fresh osteochondral allografts at six months after surgery and the resultant consequences of traditional freezing may facilitate in vivo maintenance of cartilage integrity. Our hypothesis was that the state of the allograft at implantation affects its performance after six months in vivo. Methods: The effect of frozen as compared with fresh storage on in vivo allograft performance was determined for osteochondral allografts that were transplanted into seven recipient goats and analyzed at six months. Allograft performance was assessed by examining osteochondral structure (cartilage thickness, fill, surface location, surface degeneration, and bone-cartilage interface location), zonal cartilage composition (cellularity, matrix content), and cartilage biomechanical function (stiffness). Relationships between cartilage stiffness or cartilage composition and surface degeneration were assessed with use of linear regression. Results: Fresh allografts maintained cartilage load-bearing function, while also maintaining zonal organization of cartilage cellularity and matrix content, compared with frozen allografts. Overall, allograft performance was similar between fresh allografts and nonoperative controls. However, cartilage stiffness was approximately 80% lower (95% confidence interval [CI], 73% to 87%) in the frozen allografts than in the nonoperative controls or fresh allografts. Concomitantly, in frozen allografts, matrix content and cellularity were approximately 55% (95% CI, 22% to 92%) and approximately 96% (95% CI, 94% to 99%) lower, respectively, than those in the nonoperative controls and fresh allografts. Cartilage stiffness correlated positively with cartilage cellularity and matrix content, and negatively with surface degeneration. Conclusions: Maintenance of cartilage load-bearing function in allografts is associated with zonal maintenance of cartilage cellularity and matrix content. In this animal model, frozen allografts displayed signs of failure at six months, with cartilage softening, loss of cells and matrix, and/or graft subsidence, supporting the importance of maintaining cell viability during allograft storage and suggesting that outcomes at six months may be indicative of long-term (dys)function. Clinical Relevance: Fresh versus frozen allografts represent the “best versus worst” conditions with respect to chondrocyte viability, but “difficult versus simple” with respect to acquisition and distribution. The outcomes described from these two conditions expand the current understanding of in vivo cartilage remodeling and describe structural properties (initial graft subsidence), which may have implications for impending graft failure. PMID:23138239

Potential probiotics from Indian major carp, Cirrhinus mrigala. Characterization, pathogen inhibitory activity, partial characterization of bacteriocin and production of exoenzymes.

PubMed

Mukherjee, Anjan; Dutta, Dipanjan; Banerjee, Sudeshna; Ringø, Einar; Breines, Eva Marie; Hareide, Ellinor; Chandra, Goutam; Ghosh, Koushik

2016-10-01

The study explored antagonistic activity of the cellular components of potential probiotic bacteria from mrigal (Cirrhinus mrigala) against fish pathogens with a basic insight of the chemical nature of the antagonistic compound. Totally 208 autochthonous gut bacteria were isolated, of which 22 strains revealed antagonism towards ≥2 of the six common fish pathogens. Zones of inhibition (halo diameter) were presented as score and the four most promising strains were selected as putative probiotics based on the cumulative score assigned. Further, evaluation of different cellular components exhibited bactericidal activity against the fish pathogens. Verification of other probiotic properties revealed that each of the selected strains produced diverse extra-cellular enzymes. The selected strains grew better in intestinal mucus than skin mucus, were resistant to diluted bile juice (2-20%) and safe for the target fish. The extracellular product used as crude bacteriocin revealed thermostability (up to 90°C) and activity over wide pH range (4-9). Partial loss of activity through treatment with proteinase-K and trypsin indicated proteinaceous nature of the antibacterial compound produced by the probiotic strains. 16S rRNA partial gene sequencing revealed that the four strains CM1FG7, CM1HG5, CM3FG19 and CM3HG10 were similar to Bacillus stratosphericus (KM277362), Bacillus aerophilus (KM277363), Bacillus licheniformis (KM277364) and Solibacillus silvestris (KM277365), respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tandem repeats of the 5' non-transcribed spacer of Tetrahymena rDNA function as high copy number autonomous replicons in the macronucleus but do not prevent rRNA gene dosage regulation.

PubMed Central

Pan, W J; Blackburn, E H

1995-01-01

The rRNA genes in the somatic macronucleus of Tetrahymena thermophila are normally on 21 kb linear palindromic molecules (rDNA). We examined the effect on rRNA gene dosage of transforming T.thermophila macronuclei with plasmid constructs containing a pair of tandemly repeated rDNA replication origin regions unlinked to the rRNA gene. A significant proportion of the plasmid sequences were maintained as high copy circular molecules, eventually consisting solely of tandem arrays of origin regions. As reported previously for cells transformed by a construct in which the same tandem rDNA origins were linked to the rRNA gene [Yu, G.-L. and Blackburn, E. H. (1990) Mol. Cell. Biol., 10, 2070-2080], origin sequences recombined to form linear molecules bearing several tandem repeats of the origin region, as well as rRNA genes. The total number of rDNA origin sequences eventually exceeded rRNA gene copies by approximately 20- to 40-fold and the number of circular replicons carrying only rDNA origin sequences exceeded rRNA gene copies by 2- to 3-fold. However, the rRNA gene dosage was unchanged. Hence, simply monitoring the total number of rDNA origin regions is not sufficient to regulate rRNA gene copy number. Images PMID:7784211

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania.

PubMed

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-12-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

PubMed

Szczecińska, Monika; Sawicki, Jakub

2015-09-15

The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

PubMed Central

Szczecińska, Monika; Sawicki, Jakub

2015-01-01

Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae. PMID:26389887

Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay.

PubMed

De Cecco, Marco; Jeyapalan, Jessie; Zhao, Xiaoai; Tamamori-Adachi, Mimi; Sedivy, John M

2011-10-01

Replicative cellular senescence was discovered some 50 years ago. The phenotypes of senescent cells have been investigated extensively in cell culture, and found to affect essentially all aspects of cellular physiology. The relevance of cellular senescence in the context of age-associated pathologies as well as normal aging is a topic of active and ongoing interest. Considerable effort has been devoted to biomarker discovery to enable the microscopic detection of single senescent cells in tissues. One characteristic of senescent cells documented very early in cell culture studies was an increase in cell size and total protein content, but whether this occurs in vivo is not known. A limiting factor for studies of protein content and localization has been the lack of suitable fluorescence microscopy tools. We have developed an easy and flexible method, based on the merocyanine dye known as NanoOrange, to visualize and quantitatively measure total protein levels by high resolution fluorescence microscopy. NanoOrange staining can be combined with antibody-based immunofluorescence, thus providing both specific target and total protein information in the same specimen. These methods are optimally combined with automated image analysis platforms for high throughput analysis. We document here increasing protein content and density in nuclei of senescent human and mouse fibroblasts in vitro, and in liver nuclei of aged mice in vivo. Additionally, in aged liver nuclei NanoOrange revealed protein-dense foci that colocalize with centromeric heterochromatin.

Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay

PubMed Central

De Cecco, Marco; Jeyapalan, Jessie; Zhao, Xiaoai; Tamamori-Adachi, Mimi; Sedivy, John M.

2011-01-01

Replicative cellular senescence was discovered some 50 years ago. The phenotypes of senescent cells have been investigated extensively in cell culture, and found to affect essentially all aspects of cellular physiology. The relevance of cellular senescence in the context of age-associated pathologies as well as normal aging is a topic of active and ongoing interest. Considerable effort has been devoted to biomarker discovery to enable the microscopic detection of single senescent cells in tissues. One characteristic of senescent cells documented very early in cell culture studies was an increase in cell size and total protein content, but whether this occurs in vivo is not known. A limiting factor for studies of protein content and localization has been the lack of suitable fluorescence microscopy tools. We have developed an easy and flexible method, based on the merocyanine dye known as NanoOrange, to visualize and quantitatively measure total protein levels by high resolution fluorescence microscopy. NanoOrange staining can be combined with antibody-based immunofluorescence, thus providing both specific target and total protein information in the same specimen. These methods are optimally combined with automated image analysis platforms for high throughput analysis. We document here increasing protein content and density in nuclei of senescent human and mouse fibroblasts in vitro, and in liver nuclei of aged mice in vivo. Additionally, in aged liver nuclei NanoOrange revealed protein-dense foci that colocalize with centromeric heterochromatin. PMID:22006542

Subcellular Localized Chemical Imaging of Benthic Algal Nutritional Content via HgCdTe Array FT-IR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetzel, D.; Murdock, J; Dodds, W

2008-01-01

Algae respond rapidly and uniquely to changes in nutrient availability by adjusting pigment, storage product, and organelle content and quality. Cellular and subcellular variability of the relative abundance of macromolecular pools (e.g. protein, lipid, carbohydrate, and phosphodiesters) within the benthic (bottom dwelling) alga Cladophora glomerata (a common nuisance species in fresh and saline waters) was revealed by FT-IR microspectroscopic imaging. Nutrient heterogeneity was compared at the filament, cellular, and subcellular level, and localized nutrient uptake kinetics were studied by detecting the gradual incorporation of isotopically labeled nitrogen (N) (as K15NO3) from surrounding water into cellular proteins. Nutritional content differed substantiallymore » among filament cells, with differences driven by protein and lipid abundance. Whole cell imaging showed high subcellular macromolecular variability in all cells, including adjacent cells on a filament that developed clonally. N uptake was also very heterogeneous, both within and among cells, and did not appear to coincide with subcellular protein distribution. Despite high intercellular variability, some patterns emerged. Cells acquired more 15N the further they were away from the filament attachment point, and 15N incorporation was more closely correlated with phosphodiester content than protein, lipid, or carbohydrate content. Benthic algae are subject to substantial environmental heterogeneity induced by microscale hydrodynamic factors and spatial variability in nutrient availability. Species specific responses to nutrient heterogeneity are central to understanding this key component of aquatic ecosystems. FT-IR microspectroscopy, modified for benthic algae, allows determination of algal physiological responses at scales not available using current techniques.« less

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

PubMed Central

Smirnov, Alexandre; Entelis, Nina; Martin, Robert P.; Tarassov, Ivan

2011-01-01

5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes. PMID:21685364

5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

NASA Technical Reports Server (NTRS)

Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.

1989-01-01

The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

Classification of Culturable Bifidobacterial Population from Colonic Samples of Wild Pigs (Sus scrofa) Based on Three Molecular Genetic Methods.

PubMed

Pechar, Radko; Killer, Jiří; Mekadim, Chahrazed; Geigerová, Martina; Rada, Vojtěch

2017-11-01

Occurrence of bifidobacteria, known as health-promoting probiotic microorganisms, in the digestive tract of wild pigs (Sus scrofa) has not been examined yet. One hundred forty-nine fructose-6-phosphate phosphoketolase positive bacterial strains were isolated from colonic content of twenty-two individuals of wild pigs originated from four localities in the Czechia. Based on PCR-DGGE technique targeting the variable V3 region of the 16S rRNA genes, strains were initially differentiated into four groups represented by: (i) probably a new Bifidobacterium species (89 strains), (ii) B. boum/B. thermophilum/B. thermacidophilum subsp. porcinum/B. thermacidophilum subsp. thermacidophilum (sub)species (49 strains), (iii) Pseudoscardovia suis (7 strains), and (iv) B. pseudolongum subsp. globosum/B. pseudolongum subsp. pseudolongum (4 strains), respectively. Given the fact that DGGE technique did not allow to differentiate the representatives of thermophilic bifidobacteria and B. pseudolongum subspecies, strains were further classified by the 16S rRNA and thrS gene sequences. Primers targeting the variable regions of the latter gene were designed to be applicable in identification and phylogeny of Bifidobacteriaceae family. The 16S rRNA-derived phylogenetic study classified members of the first group into five subgroups in a separated cluster of thermophilic bifidobacteria. Comparable results were obtained by the thrS-derived phylogenetic analysis. Remarkably, variability among thrS sequences was higher compared with 16S rRNA gene sequences. Overall, molecular genetic techniques application allowed to identify a new Bifidobacterium phylotype which is predominant in the digestive tract of examined wild pigs.

Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

PubMed Central

Maier, Uwe-G; Zauner, Stefan; Woehle, Christian; Bolte, Kathrin; Hempel, Franziska; Allen, John F.; Martin, William F.

2013-01-01

Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force. PMID:24259312

Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.

PubMed

Gu, Chun Tao; Li, Chun Yan; Yang, Li Jie; Huo, Gui Cheng

2014-08-01

A Gram-stain-negative bacterial strain, 10-17(T), was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 10-17(T) was phylogenetically related to Enterobacter hormaechei CIP 103441(T), Enterobacter cancerogenus LMG 2693(T), Enterobacter asburiae JCM 6051(T), Enterobacter mori LMG 25706(T), Enterobacter ludwigii EN-119(T) and Leclercia adecarboxylata LMG 2803(T), having 99.5%, 99.3%, 98.7%, 98.5%, 98.4% and 98.4% 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17(T) ( = LMG 27195(T) = NCIMB 14836(T) = CCUG 62994(T)). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1(T)( = CGMCC 1.12102(T) = LMG 26783(T)). © 2014 IUMS.

Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations.

PubMed

Nocker, Andreas; Lepo, Joe Eugene; Martin, Linda Lin; Snyder, Richard Allan

2007-10-01

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.

Sulfur-inhibited Thermosphaera aggregans sp. nov., a new genus of hyperthermophilic archaea isolated after its prediction from environmentally derived 16S rRNA sequences.

PubMed

Huber, R; Dyba, D; Huber, H; Burggraf, S; Rachel, R

1998-01-01

Recently, a new procedure was developed which allowed for the first time the isolation of a hyperthermophilic archaeum tracked by 165 rRNA analysis from a terrestrial hot solfataric spring ('Obsidian Pool', Yellowstone National Park, WY, USA). This novel isolate is characterized here. Cells are round cocci with a diameter of 0.2-0.8 micron, occurring singly, in pairs, short chains and in grape-like aggregates. The aggregates exhibit a weak bluish-green fluorescence under UV radiation at 420 nm. The new isolate is an anaerobic obligate heterotroph, using preferentially yeast extract for growth. The metabolic products include CO2, H2, acetate and isovalerate. Growth is observed between 65 and 90 degrees C (optimum: 85 degrees C), from pH 5.0 to 7.0 (optimum: 6.5) and up to 0.7% NaCl. The apparent activation energy for growth is about 149 kJ mol-1. Elemental sulfur or hydrogen inhibits growth. The core lipids consist mainly of acyclic and cyclic glycerol diphytanyl tetraethers. The cell envelope contains a cytoplasmic membrane covered by an amorphous layer of unknown composition; there is no evidence for a regularly arrayed surface-layer protein. The G + C content is 46 mol%. On the basis of 165 rRNA sequence comparisons in combination with morphological, physiological and biochemical properties, the isolate represents a new genus within the Desulfurococcaceae, which has been named Thermosphaera. The type species is Thermosphaera aggregans, the type strain is isolate M11TLT (= DSM 11486T).

Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water.

PubMed

Gallego, Virginia; García, María Teresa; Ventosa, Antonio

2005-01-01

Members of the genus Methylobacterium are ubiquitous in nature and can be isolated from almost any freshwater environment where dissolved oxygen exists. This genus is composed of a variety of pink-pigmented, facultatively methylotrophic (PPFM) bacteria. During a screening programme to monitor the bacterial population present in the drinking water of a municipal water supply in Seville (Spain) during the year 2003, five strains of PPFM bacteria were isolated and characterized. Analysis of their complete 16S rRNA gene sequences revealed that they constituted two separate phylogenetic groups (strains GP34T and GR18, and strains GR16T, GP22 and GP32, respectively) showing highest similarity to members of the genus Methylobacterium. The highest 16S rRNA sequence similarities of strain GP34T were found with respect to the type strains of Methylobacterium radiotolerans (96.6 %) and Methylobacterium fujisawaense (96.4 %) and the highest 16S rRNA sequence similarities of strain GR16T were to the type strains of Methylobacterium extorquens (96.0 %) and Methylobacterium rhodesianum (95.8 %). The G+C content of their DNA ranged from 66.5 to 67.8 mol%. DNA-DNA hybridization studies confirmed that they constituted two separate genospecies. On the basis of this phenotypic, phylogenetic and genotypic study, two novel species of the genus Methylobacterium are proposed: Methylobacterium hispanicum sp. nov., with type strain GP34T (CECT 5997T=CCM 7219T=DSM 16372T=CIP 108332T), and Methylobacterium aquaticum sp. nov., with type strain GR16T (CECT 5998T=CCM 7218T=DSM 16371T=CIP 108333T).

Paenibacillus brassicae sp. nov., isolated from cabbage rhizosphere in Beijing, China.

PubMed

Gao, Miao; Yang, Hui; Zhao, Ji; Liu, Jun; Sun, Yan-hua; Wang, Yu-jiong; Sun, Jian-guang

2013-03-01

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 112(T), was isolated from cabbage rhizosphere in Beijing, China. The strain was found to grow at 10-40 °C and pH 4-11, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on a fragment of the full-length 16S rRNA gene sequence revealed that strain 112(T) is a member of the genus Paenibacillus. High levels of 16S rRNA gene similarities were found between strain 112(T), Paenibacillus sabinae DSM 17841(T) (97.82 %) and Paenibacillus forsythiae DSM 17842(T) (97.22 %). However, the DNA-DNA hybridization values between strain 112(T) and the type strains of these two species were 10.36 and 6.28 %, respectively. The predominant menaquinone was found to be menaquinone 7 (MK-7). The major fatty acids were determined to be anteiso-C(15:0) and C(16:0). The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The DNA G+C content was determined to be 55.4 mol%. On the basis of its phenotypic characteristics, 16S rRNA gene sequence analysis and the value of DNA-DNA hybridization, strain 112(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus brassicae sp. nov. is proposed. The type strain is 112(T) (= ACCC 01125(T) = DSM 24983(T)).

Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room.

PubMed

Vaishampayan, Parag; Probst, Alexander; Krishnamurthi, Srinivasan; Ghosh, Sudeshna; Osman, Shariff; McDowall, Alasdair; Ruckmani, Arunachalam; Mayilraj, Shanmugam; Venkateswaran, Kasthuri

2010-05-01

Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m(-2). The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA-DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA-DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6+/-0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SC(T) (=NRRL B-59162(T) =MTCC 9535(T)).

Identification of an Alternative rRNA Post-transcriptional Maturation of 26S rRNA in the Kingdom Fungi.

PubMed

Navarro-Ródenas, Alfonso; Carra, Andrea; Morte, Asunción

2018-01-01

Despite of the integrity of their RNA, some desert truffles present a non-canonical profile of rRNA where 3.3 kb is absent, 1.8 kb is clear and a band of 1.6 kb is observed. A similar rRNA profile was identified in organisms belonging to different life kingdoms, with the exception of the Kingdom Fungi, as a result of a split LSU rRNA called hidden gap . rRNA profiles of desert truffles were analyzed to verify the presence of the non-canonical profile. The RNA of desert truffles and yeast were blotted and hybridized with probes complementary to LSU extremes. RACE of LSU rRNA was carried out to determine the LSU rRNA breakage point. LSU rRNA of desert truffles presents a post-transcriptional cleavage of five nucleotides that generates a hidden gap located in domain D7. LSU splits into two molecules of 1.6 and 1.8 kb. Similar to other organisms, a UAAU tract, downstream of the breakage point, was identified. Phylogenetic comparison suggests that during fungi evolution mutations were introduced in the hypervariable D7 domain, resulting in a sequence that is specifically post-transcriptionally cleaved in some desert truffles.

Coupled transcription and processing of mouse ribosomal RNA in a cell-free system.

PubMed Central

Mishima, Y; Mitsuma, T; Ogata, K

1985-01-01

An in vitro processing system of mouse rRNA was achieved using an RNA polymerase I-specific transcription system, (S100) and recombinant plasmids consisting of mouse rRNA gene (rDNA) segments containing the transcription initiation and 5'-terminal region of 18S (or 41S) rRNA. Pulse-chase experiments showed that a specific processing occurred with transcripts of the plasmid DNAs when the direction of transcription was the correct orientation relative to the 18S rRNA coding sequence, but not with transcripts of the DNA templates in which this coding sequence was in the opposite orientation. From the S1 nuclease protection analyses, we concluded that there are several steps of endonucleolytic cleavage including one 105 nucleotides upstream from the 5' end of 18S rRNA. Intermediates cleaved at this site were identified in in vivo processing of rRNA. This result indicates that endonucleolytic cleavage takes place 105 nucleotides upstream from the 5' terminus of 18S rRNA prior to the formation of mature 18S rRNA. Trimming or cleavage of the 105 nucleotides may be involved in the formation of the 5' terminus of mature 18S rRNA. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:3004977

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania

PubMed Central

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-01-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved. PMID:22767185

Defining the RNA-Protein Interactions in the Trypanosome Preribosomal Complex

PubMed Central

Wang, Lei; Ciganda, Martin

2013-01-01

In eukaryotes, 5S rRNA is transcribed in the nucleoplasm and requires the ribosomal protein L5 to deliver it to the nucleolus for ribosomal assembly. The trypanosome-specific proteins P34 and P37 form a novel preribosomal complex with the eukaryotic conserved L5-5S rRNA complex in the nucleoplasm. Previous results suggested that P34 acts together with L5 to bridge the interaction with 5S rRNA and thus to stabilize 5S rRNA, an important role in the early steps of ribosomal biogenesis. Here, we have delineated the domains of the two protein components, L5 and P34, and regions of the RNA partner, 5S rRNA, that are critical for protein-RNA interactions within the complex. We found that the L18 domain of L5 and the N terminus and RNA recognition motif of P34 bind 5S rRNA. We showed that Trypanosoma brucei L5 binds the β arm of 5S rRNA, while P34 binds loop A/stem V of 5S rRNA. We demonstrated that 5S rRNA is able to enhance the association between the protein components of the complex, L5 and P34. Both loop A/stem V and the β arm of 5S rRNA can separately enhance the protein-protein association, but their effects are neither additive nor synergistic. Domains in the two proteins for protein-protein and protein-RNA interactions overlap or are close to each other. This suggests that 5S rRNA binding might cause conformational changes in L5 and P34 and might also bridge the interactions, thus enhancing binding between the protein partners of this novel complex. PMID:23397568

Mechanisms for ribotoxin-induced ribosomal RNA cleavage

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Kaiyu; Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824; Zhou, Hui-Ren

The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activatedmore » kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via activation of p53, caspases and cathepsins. ► DON- and anisomycin-triggered rRNA cleavage is p38-dependent. ► SG- and ricin-induced rRNA cleavage is p38-independent.« less

Finding Toxicological Tipping Points from High-Content Imaging Data (WC10)

EPA Science Inventory

A key challenge to using in vitro data in risk assessment is differentiating between chemical-induced adaptive versus adverse cellular responses. To further investigate this issue, we studied the effects of hundreds of chemicals in HepG2 cells using high-content imaging (HCI). HC...

Leuconostoc pseudomesenteroides WCFur3 partial 16S rRNA gene

USDA-ARS?s Scientific Manuscript database

This study used a partial 535 base pair 16S rRNA gene sequence to identify a bacterial isolate. Fatty acid profiles are consistent with the 16S rRNA gene sequence identification of this bacterium. The isolate was obtained from a compost bin in Fort Collins, Colorado, USA. The 16S rRNA gene sequen...

Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function.

PubMed

He, Yue; Yam, Candice; Pomraning, Kyle; Chin, Jacqueline S R; Yew, Joanne Y; Freitag, Michael; Oliferenko, Snezhana

2014-12-15

Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway. © 2014 He, Yam, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

The first complete organellar genomes of an Antarctic red alga, Pyropia endiviifolia: insights into its genome architecture and phylogenetic position within genus Pyropia (Bangiales, Rhodophyta)

NASA Astrophysics Data System (ADS)

Xu, Kuipeng; Tang, Xianghai; Bi, Guiqi; Cao, Min; Wang, Lu; Mao, Yunxiang

2017-08-01

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes (ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome (195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome (34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the ptDNA and group II introns in the mtDNA. The other Pyropia species have 2u20133 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.

Estimation of the Relative Abundance of Different Bacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences

PubMed Central

Wood, Jacqueline; Scott, Karen P.; Avguštin, Gorazd; Newbold, C. James; Flint, Harry J.

1998-01-01

We describe an approach for determining the genetic composition of Bacteroides and Prevotella populations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides and Prevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution of Bacteroides and Prevotella sequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA. Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotella strains, together accounted for between 20 and 86% of the total amplified Bacteroides and Prevotella rDNA in these samples. The most abundant Bacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundant Bacteroides and Prevotella groups in the rumen are underrepresented among cultured rumen Prevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples. PMID:9758785

Correlation analyses of phytochemical composition, chemical, and cellular measures of antioxidant activity of broccoli (Brassica oleracea L. Var. italica).

PubMed

Eberhardt, Marian V; Kobira, Kanta; Keck, Anna-Sigrid; Juvik, John A; Jeffery, Elizabeth H

2005-09-21

Chemical measures of antioxidant activity within the plant, such as the oxygen radical absorbance capacity (ORAC) assay, have been reported for many plant-based foods. However, the extent to which chemical measures relate to cellular measures of oxidative stress is unclear. The natural variation in the phytochemical content of 22 broccoli genotypes was used to determine correlations among chemical composition (carotenoids, tocopherols and polyphenolics), chemical antioxidant activity (ORAC), and measures of cellular antioxidation [prevention of DNA oxidative damage and of oxidation of the biomarker dichlorofluorescein (DCFH) in HepG2 cells] using hydrophilic and lipophilic extracts of broccoli. For lipophilic extracts, ORAC (ORAC-L) correlated with inhibition of cellular oxidation of DCFH (DCFH-L, r = 0.596, p = 0.006). Also, DNA damage in the presence of the lipophilic extract was negatively correlated with both chemical and cellular measures of antioxidant activity as measured by ORAC-L (r = -0.705, p = 0.015) and DCFH-L (r = -0.671, p = 0.048), respectively. However, no correlations were observed for hydrophilic (-H) extracts, except between polyphenol content and ORAC (ORAC-H; r = 0.778, p < 0.001). Inhibition of cellular oxidation by hydrophilic extracts (DCFH-H) and ORAC-H were approximately 8- and 4-fold greater than DCFH-L and ORAC-L, respectively. Whether ORAC-H has more biological relevance than ORAC-L because of its magnitude or whether ORAC-L bears more biological relevance because it relates to cellular estimates of antioxidant activity remains to be determined. Chemical estimates of antioxidant capacity within the plant may not accurately reflect the complex nature of the full antioxidant activity of broccoli extracts within cells.

Effect of Nitrogen on Cellular Production and Release of the Neurotoxin Anatoxin-A in a Nitrogen-Fixing Cyanobacterium

PubMed Central

Gagnon, Alexis; Pick, Frances R.

2012-01-01

Anatoxin-a (ANTX) is a neurotoxin produced by several freshwater cyanobacteria and implicated in lethal poisonings of domesticated animals and wildlife. The factors leading to its production in nature and in culture are not well understood. Resource availability may influence its cellular production as suggested by the carbon-nutrient hypothesis, which links the amount of secondary metabolites produced by plants or microbes to the relative abundance of nutrients. We tested the effects of nitrogen supply (as 1, 5, and 100% N of standard cyanobacterial medium corresponding to 15, 75, and 1500 mg L−1 of NaNO3 respectively) on ANTX production and release in a toxic strain of the planktonic cyanobacterium Aphanizomenon issatschenkoi (Nostocales). We hypothesized that nitrogen deficiency might constrain the production of ANTX. However, the total concentration and more significantly the cellular content of anatoxin-a peaked (max. 146 μg/L and 1683 μg g−1 dry weight) at intermediate levels of nitrogen supply when N-deficiency was evident based on phycocyanin to chlorophyll a and carbon to nitrogen ratios. The results suggest that the cellular production of anatoxin-a may be stimulated by moderate nitrogen stress. Maximal cellular contents of other cyanotoxins have recently been reported under severe stress conditions in another Nostocales species. PMID:22701451

BacDive--The Bacterial Diversity Metadatabase in 2016.

PubMed

Söhngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz Christian; Ebeling, Christian; Pendarovski, Cezar; Overmann, Jörg

2016-01-04

BacDive-the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. The majority of data is manually annotated and curated. Currently (with release 9/2015), BacDive covers 53 978 strains. Newly implemented RESTful web services provide instant access to the content in machine-readable XML and JSON format. Besides an overall increase of data content, BacDive offers new data fields and features, e.g. the search for gene names, plasmids or 16S rRNA in the advanced search, as well as improved linkage of entries to external life science web resources. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Suppressive effects of carotenoids on the antigen-induced degranulation in RBL-2H3 rat basophilic leukemia cells.

PubMed

Manabe, Yuki; Hirata, Takashi; Sugawara, Tatsuya

2014-01-01

In this study, the anti-degranulation effects of fifteen carotenoids were evaluated using RBL-2H3 rat basophilic leukemia cell line as a mast cell model. Nine carotenoids, fucoxanthin, zeaxanthin, β-carotene, astaxanthin, 3-hydroxyechinenone, fucoxanthinol, lycopene, β-cryptoxanthin, and siphonaxanthin significantly suppressed antigen-induced mast cell degranulation. Under the same conditions, the cellular carotenoid contents were quantified using high performance liquid chromatography-photodiode array (HPLC-PDA). There was no correlation between the cellular carotenoid contents and their anti-degranulation activities. These results indicate that the differences in the anti-degranulation activities of carotenoids were not related to their uptake by the cells.

Automated microscopy for high-content RNAi screening

PubMed Central

2010-01-01

Fluorescence microscopy is one of the most powerful tools to investigate complex cellular processes such as cell division, cell motility, or intracellular trafficking. The availability of RNA interference (RNAi) technology and automated microscopy has opened the possibility to perform cellular imaging in functional genomics and other large-scale applications. Although imaging often dramatically increases the content of a screening assay, it poses new challenges to achieve accurate quantitative annotation and therefore needs to be carefully adjusted to the specific needs of individual screening applications. In this review, we discuss principles of assay design, large-scale RNAi, microscope automation, and computational data analysis. We highlight strategies for imaging-based RNAi screening adapted to different library and assay designs. PMID:20176920

Distinction of broken cellular wall Ganoderma lucidum spores and G. lucidum spores using FTIR microspectroscopy

NASA Astrophysics Data System (ADS)

Chen, Xianliang; Liu, Xingcun; Sheng, Daping; Huang, Dake; Li, Weizu; Wang, Xin

2012-11-01

In this paper, FTIR microspectroscopy was used to identify broken cellular wall Ganoderma lucidum spores and G. lucidum spores. For IR spectra, broken cellular wall G. lucidum spores and G. lucidum spores were mainly different in the regions of 3000-2800, 1660-1600, 1400-1200 and 1100-1000 cm-1. For curve fitting, the results showed the differences in the protein secondary structures and the polysaccharide structures/content between broken cellular wall G. lucidum spores and G. lucidum spores. Moreover, the value of A1078/A1741 might be a potentially useful factor to distinguish broken cellular wall G. lucidum spores from G. lucidum spores. Additionally, FTIR microspectroscopy could identify broken cellular wall G. lucidum spores and G. lucidum spores accurately when it was combined with hierarchical cluster analysis. The result suggests FTIR microspectroscopy is very simple and efficient for distinction of broken cellular wall G. lucidum spores and G. lucidum spores. The result also indicates FTIR microspectroscopy may be useful for TCM identification.

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

PubMed Central

Petrova, Olga E.; Garcia-Alcalde, Fernando; Zampaloni, Claudia; Sauer, Karin

2017-01-01

Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, comparative evaluation of bacterial rRNA depletion methods has remained limited. Moreover, no such study has utilized RNA derived from bacterial biofilms, which have potentially higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis. Presently, we evaluated the efficiency of three subtractive hybridization-based kits in depleting rRNA from samples derived from biofilm, as well as planktonic cells of the opportunistic human pathogen Pseudomonas aeruginosa. Our results indicated different rRNA removal efficiency for the three procedures, with the Ribo-Zero kit yielding the highest degree of rRNA depletion, which translated into enhanced enrichment of non-rRNA transcripts and increased depth of RNA-seq coverage. The results indicated that, in addition to improving RNA-seq sensitivity, efficient rRNA removal enhanced detection of low abundance transcripts via qPCR. Finally, we demonstrate that the Ribo-Zero kit also exhibited the highest efficiency when P. aeruginosa/Staphylococcus aureus co-culture RNA samples were tested. PMID:28117413

Dropping macadamia nuts-in-shell reduces kernel roasting quality.

PubMed

Walton, David A; Wallace, Helen M

2010-10-01

Macadamia nuts ('nuts-in-shell') are subjected to many impacts from dropping during postharvest handling, resulting in damage to the raw kernel. The effect of dropping on roasted kernel quality is unknown. Macadamia nuts-in-shell were dropped in various combinations of moisture content, number of drops and receiving surface in three experiments. After dropping, samples from each treatment and undropped controls were dry oven-roasted for 20 min at 130 °C, and kernels were assessed for colour, mottled colour and surface damage. Dropping nuts-in-shell onto a bed of nuts-in-shell at 3% moisture content or 20% moisture content increased the percentage of dark roasted kernels. Kernels from nuts dropped first at 20%, then 10% moisture content, onto a metal plate had increased mottled colour. Dropping nuts-in-shell at 3% moisture content onto nuts-in-shell significantly increased surface damage. Similarly, surface damage increased for kernels dropped onto a metal plate at 20%, then at 10% moisture content. Postharvest dropping of macadamia nuts-in-shell causes concealed cellular damage to kernels, the effects not evident until roasting. This damage provides the reagents needed for non-enzymatic browning reactions. Improvements in handling, such as reducing the number of drops and improving handling equipment, will reduce cellular damage and after-roast darkening. Copyright © 2010 Society of Chemical Industry.

5S rRNA and ribosome.

PubMed

Gongadze, G M

2011-12-01

5S rRNA is an integral component of the ribosome of all living organisms. It is known that the ribosome without 5S rRNA is functionally inactive. However, the question about the specific role of this RNA in functioning of the translation apparatus is still open. This review presents a brief history of the discovery of 5S rRNA and studies of its origin and localization in the ribosome. The previously expressed hypotheses about the role of this RNA in the functioning of the ribosome are discussed considering the unique location of 5S rRNA in the ribosome and its intermolecular contacts. Based on analysis of the current data on ribosome structure and its functional complexes, the role of 5S rRNA as an intermediary between ribosome functional domains is discussed.

G protein-coupled receptor internalization assays in the high-content screening format.

PubMed

Haasen, Dorothea; Schnapp, Andreas; Valler, Martin J; Heilker, Ralf

2006-01-01

High-content screening (HCS), a combination of fluorescence microscopic imaging and automated image analysis, has become a frequently applied tool to study test compound effects in cellular disease-modeling systems. This chapter describes the measurement of G protein-coupled receptor (GPCR) internalization in the HCS format using a high-throughput, confocal cellular imaging device. GPCRs are the most successful group of therapeutic targets on the pharmaceutical market. Accordingly, the search for compounds that interfere with GPCR function in a specific and selective way is a major focus of the pharmaceutical industry today. This chapter describes methods for the ligand-induced internalization of GPCRs labeled previously with either a fluorophore-conjugated ligand or an antibody directed against an N-terminal tag of the GPCR. Both labeling techniques produce robust assay formats. Complementary to other functional GPCR drug discovery assays, internalization assays enable a pharmacological analysis of test compounds. We conclude that GPCR internalization assays represent a valuable medium/high-throughput screening format to determine the cellular activity of GPCR ligands.

Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases

PubMed Central

Lin, Chen; Mak, Wayne; Hong, Pengyu; Sepp, Katharine; Perrimon, Norbert

2010-01-01

Recently, High-content screening (HCS) has been combined with RNA interference (RNAi) to become an essential image-based high-throughput method for studying genes and biological networks through RNAi-induced cellular phenotype analyses. However, a genome-wide RNAi-HCS screen typically generates tens of thousands of images, most of which remain uncategorized due to the inadequacies of existing HCS image analysis tools. Until now, it still requires highly trained scientists to browse a prohibitively large RNAi-HCS image database and produce only a handful of qualitative results regarding cellular morphological phenotypes. For this reason we have developed intelligent interfaces to facilitate the application of the HCS technology in biomedical research. Our new interfaces empower biologists with computational power not only to effectively and efficiently explore large-scale RNAi-HCS image databases, but also to apply their knowledge and experience to interactive mining of cellular phenotypes using Content-Based Image Retrieval (CBIR) with Relevance Feedback (RF) techniques. PMID:21278820

Identification of a Recently Active Mammalian SINE Derived from Ribosomal RNA

PubMed Central

Longo, Mark S.; Brown, Judy D.; Zhang, Chu; O’Neill, Michael J.; O’Neill, Rachel J.

2015-01-01

Complex eukaryotic genomes are riddled with repeated sequences whose derivation does not coincide with phylogenetic history and thus is often unknown. Among such sequences, the capacity for transcriptional activity coupled with the adaptive use of reverse transcription can lead to a diverse group of genomic elements across taxa, otherwise known as selfish elements or mobile elements. Short interspersed nuclear elements (SINEs) are nonautonomous mobile elements found in eukaryotic genomes, typically derived from cellular RNAs such as tRNAs, 7SL or 5S rRNA. Here, we identify and characterize a previously unknown SINE derived from the 3′-end of the large ribosomal subunit (LSU or 28S rDNA) and transcribed via RNA polymerase III. This new element, SINE28, is represented in low-copy numbers in the human reference genome assembly, wherein we have identified 27 discrete loci. Phylogenetic analysis indicates these elements have been transpositionally active within primate lineages as recently as 6 MYA while modern humans still carry transcriptionally active copies. Moreover, we have identified SINE28s in all currently available assembled mammalian genome sequences. Phylogenetic comparisons indicate that these elements are frequently rederived from the highly conserved LSU rRNA sequences in a lineage-specific manner. We propose that this element has not been previously recognized as a SINE given its high identity to the canonical LSU, and that SINE28 likely represents one of possibly many unidentified, active transposable elements within mammalian genomes. PMID:25637222

LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions

PubMed Central

Liu, Xiuju; Huang, Henry; Wilkinson, Scott C.; Zhong, Diansheng; Khuri, Fadlo R.; Fu, Haian; Marcus, Adam; He, Yulong; Zhou, Wei

2016-01-01

We analyzed the mechanism underlying 5-aminoimidazole-4-carboxamide riboside (AICAR) mediated apoptosis in LKB1-null non-small cell lung cancer (NSCLC) cells. Metabolic profile analysis revealed depletion of the intracellular pyrimidine pool after AICAR treatment, but uridine was the only nucleotide precursor capable of rescuing this apoptosis, suggesting the involvement of RNA metabolism. Because half of RNA transcription in cancer is for pre-ribosomal RNA (rRNA) synthesis, which is suppressed by over 90% after AICAR treatment, we evaluated the role of TIF-IA-mediated rRNA synthesis. While the depletion of TIF-IA by RNAi alone promoted apoptosis in LKB1-null cells, the overexpression of a wild-type or a S636A TIF-IA mutant, but not a S636D mutant, attenuated AICAR-induced apoptosis. In LKB1-null H157 cells, pre-rRNA synthesis was not suppressed by AICAR when wild-type LKB1 was present, and cellular fractionation analysis indicated that TIF-IA quickly accumulated in the nucleus in the presence of a wild-type LKB1 but not a kinase-dead mutant. Furthermore, ectopic expression of LKB1 was capable of attenuating AICAR-induced death in AMPK-null cells. Because LKB1 promotes cell survival by modulating TIF-IA-mediated pre-rRNA synthesis, this discovery suggested that targeted depletion of uridine related metabolites may be exploited in the clinic to eliminate LKB1-null cancer cells. PMID:26506235

LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions.

PubMed

Liu, Fakeng; Jin, Rui; Liu, Xiuju; Huang, Henry; Wilkinson, Scott C; Zhong, Diansheng; Khuri, Fadlo R; Fu, Haian; Marcus, Adam; He, Yulong; Zhou, Wei

2016-01-19

We analyzed the mechanism underlying 5-aminoimidazole-4-carboxamide riboside (AICAR) mediated apoptosis in LKB1-null non-small cell lung cancer (NSCLC) cells. Metabolic profile analysis revealed depletion of the intracellular pyrimidine pool after AICAR treatment, but uridine was the only nucleotide precursor capable of rescuing this apoptosis, suggesting the involvement of RNA metabolism. Because half of RNA transcription in cancer is for pre-ribosomal RNA (rRNA) synthesis, which is suppressed by over 90% after AICAR treatment, we evaluated the role of TIF-IA-mediated rRNA synthesis. While the depletion of TIF-IA by RNAi alone promoted apoptosis in LKB1-null cells, the overexpression of a wild-type or a S636A TIF-IA mutant, but not a S636D mutant, attenuated AICAR-induced apoptosis. In LKB1-null H157 cells, pre-rRNA synthesis was not suppressed by AICAR when wild-type LKB1 was present, and cellular fractionation analysis indicated that TIF-IA quickly accumulated in the nucleus in the presence of a wild-type LKB1 but not a kinase-dead mutant. Furthermore, ectopic expression of LKB1 was capable of attenuating AICAR-induced death in AMPK-null cells. Because LKB1 promotes cell survival by modulating TIF-IA-mediated pre-rRNA synthesis, this discovery suggested that targeted depletion of uridine related metabolites may be exploited in the clinic to eliminate LKB1-null cancer cells.

Glucerabacter canisensis gen. nov., sp. nov., isolated from dog feces and its effect on the hydrolysis of plant glucosylceramide in the intestine of dogs.

PubMed

Kawata, Misho; Tsukamoto, Ami; Isozaki, Ryohei; Nobukawa, Shohei; Kawahara, Natsuki; Akutsu, Shoko; Suzuki, Masato; Asanuma, Narito

2018-04-01

A Gram-positive, obligately anaerobic, oval-rod shaped, non-spore-forming, and non-pigmented bacterium, designated strain NATH-2371 T (= JCM31739 T  = DSM105698 T ), was isolated from dog feces. Comparative 16S rRNA gene sequence analysis revealed that strain NATH-2371 T belongs to Clostridium cluster XIVa, and the closest strains were Coprococcus comes ATCC 27758 T (94.8% 16S rRNA gene sequence similarity) and Clostridium nexile DSM 1787 T (94.0%). Strain NATH-2371 T produced acetate, formate, and ethanol from glucose. Predominant cellular fatty acids are C 16:0 and C 16:0 DMA. On the basis of the phenotypic and genotypic differences, strain NATH-2371 T represents a novel species in a new genus of the family Lachnospiraceae, for which the name Glucerabacter canisensis gen. nov., sp. nov., is proposed. This strain was found to efficiently hydrolyze plant glucosylceramide (GluCer). The abundance of strain NATH-2371 T in dog feces was higher in young dogs than in old dogs. Incubation of dog fecal bacteria showed that GluCer-hydrolyzing activity decreased with the age of dogs. The cell number of strain NATH-2371 T in dog feces appeared to be correlated with GluCer hydrolysis. Thus, this bacterium is likely to play a major role in GluCer hydrolysis in the dog intestine.

Streptomyces verrucosisporus sp. nov., isolated from marine sediments.

PubMed

Phongsopitanun, Wongsakorn; Kudo, Takuji; Ohkuma, Moriya; Pittayakhajonwut, Pattama; Suwanborirux, Khanit; Tanasupawat, Somboon

2016-09-01

Five actinomycete isolates, CPB1-1T, CPB2-10, BM1-4, CPB3-1 and CPB1-18, belonging to the genus Streptomyces were isolated from marine sediments collected from Chumphon Province, Thailand. They produced open loops of warty spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in their whole-cell hydrolysates. Polar lipids found were diphosphatidylglycerol, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Menaquinones were MK-9(H6), MK-9(H8), MK-10(H6) and MK-10(H8). Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The taxonomic position of the strains was described using a polyphasic approach. blastn analysis of the 16S rRNA gene sequence revealed that these five strains exhibited the highest similarities with 'Streptomyces mangrovicola' GY1 (99.0 %), Streptomyces fenghuangensisGIMN4.003T (98.6 %), Streptomyces barkulensisRC 1831T (98.5 %) and Streptomyces radiopugnans R97T (98.3 %). However, their phenotypic characteristics and 16S rRNA gene sequences as well as DNA-DNA relatedness differentiated these five strains from the other species of the genus Streptomyces. Here, we propose the novel actinomycetes all being representatives of the same novel species, Streptomyces verrucosisporus, with type strain CPB1-1T (=JCM 18519T=PCU 343T=TISTR 2344T).

Analysis of the RNA Content of the Yeast "Saccharomyces Cerevisiae"

ERIC Educational Resources Information Center

Deutch, Charles E.; Marshall, Pamela A.

2008-01-01

In this article, the authors describe an interconnected set of relatively simple laboratory experiments in which students determine the RNA content of yeast cells and use agarose gel electrophoresis to separate and analyze the major species of cellular RNA. This set of experiments focuses on RNAs from the yeast "Saccharomyces cerevisiae", a…

Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas.

PubMed

Yabuuchi, E; Kosako, Y; Naka, T; Suzuki, S; Yano, I

1999-01-01

Based on the results of a phylogenetic analysis of 16S rRNA and the presence of sphingoglycolipid in cellular lipids of the type strains, transfer of "Rhizomonas" suberifaciens, Blastomonas natatoria and Erythromonas ursincola to the genus Sphingomonas as Sphingomonas suberifaciens (van Bruggen et al 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., and Sphingomonas ursincola (Yurkov et al 1997) comb. nov. are herein proposed together with the emendation of genus Sphingomonas. The type strain of S. suberifaciens is van Bruggen Cal=ATCC 49382=NCPPB 3629=IFO 15211=JCM 8521, that of S. natatoria is ATCC 35951 =DSM 3183=NCIMB 12085=JCM10396, and that of S. ursincola is DSM 9006= KR-99.

Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.

PubMed

Yabuuchi, E; Yano, I; Oyaizu, H; Hashimoto, Y; Ezaki, T; Yamamoto, H

1990-01-01

Based on the partial nucleotide sequence analysis of 16S ribosomal ribonucleic acid (rRNA), presence of unique sphingoglycolipids in cellular lipid, and the major type of ubiquinone (Q10), we propose Sphingomonas gen. nov. with the type species Sphingomonas paucimobilis (Holmes et al, 1977) comb. nov. From the homology values of deoxyribonucleic acid-deoxyribonucleic acid hybridization and the phenotypic characteristics, three new species, Sphingomonas parapaucimobilis, Sphingomonas yanoikuyae, Sphingomonas adhaesiva, and one new combination, Sphingomonas capsulata, are described. S. parapaucimobilis JCM 7510 (= GIFU 11387), S. yanoikuyae JCM 7371 (= GIFU 9882), and S. adhaesiva JCM 7370 (= GIFU 11458) are designated as the type strains of the three new species. Emended description of the type strain of S. capsulata is presented.

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript.

PubMed Central

Veldman, G M; Klootwijk, J; van Heerikhuizen, H; Planta, R J

1981-01-01

We have determined the nucleotide sequence of part of a cloned yeast ribosomal RNA operon extending from the 5.8S RNA gene downstream into the 5' -terminal region of the 26S RNA gene. We mapped the pertinent processing sites, viz. the 5' end of 26S rRNA and the 3'ends of 5.8S rRNA and its immediate precursor, 7S RNA. At the 3' end of 7S RNA we find the sequence UCGUUU which is very similar to the type I consensus sequence UCAUUA/U present at the 3' ends of 17S, 5.8S and 26S rRNA as well as 18S precursor rRNA in yeast. At the 5' end of the 26S RNA gene we find a sequence of thirteen nucleotides which is homologous to the type II sequence present at the 5' termini of both the 17S and the 5.8S RNA gene. These findings further support the suggestion put forward earlier (G.M. Veldman et al. (1980) Nucl. Acids Res. 8, 2907-2920) that both consensus sequences are involved in the recognition of precursor rRNA by the processing nuclease(s). We discuss a model for the processing of yeast rRNA in which a processing enzyme sequentially recognizes several combinations of a type I and a type II consensus sequence. We also describe the existence of a significant base complementarity between sequences in the 5' -terminal region of 26S rRNA and the 3' -terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA. Images PMID:7312619

Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro

PubMed Central

Sharwood, Robert E.; Hotto, Amber M.; Bollenbach, Thomas J.; Stern, David B.

2011-01-01

Post-transcriptional regulation in the chloroplast is exerted by nucleus-encoded ribonucleases and RNA-binding proteins. One of these ribonucleases is RNR1, a 3′-to-5′ exoribonuclease of the RNase II family. We have previously shown that Arabidopsis rnr1-null mutants exhibit specific abnormalities in the expression of the rRNA operon, including the accumulation of precursor 23S, 16S, and 4.5S species and a concomitant decrease in the mature species. 5S rRNA transcripts, however, accumulate to a very low level in both precursor and mature forms, suggesting that they are unstable in the rnr1 background. Here we demonstrate that rnr1 plants overaccumulate an antisense RNA, AS5, that is complementary to the 5S rRNA, its intergenic spacer, and the downstream trnR gene, which encodes tRNAArg, raising the possibility that AS5 destabilizes 5S rRNA or its precursor and/or blocks rRNA maturation. To investigate this, we used an in vitro system that supports 5S rRNA and trnR processing. We show that AS5 inhibits 5S rRNA maturation from a 5S-trnR precursor, and shorter versions of AS5 demonstrate that inhibition requires intergenic sequences. To test whether the sense and antisense RNAs form double-stranded regions in vitro, treatment with the single-strand-specific mung bean nuclease was used. These results suggest that 5S–AS5 duplexes interfere with a sense-strand secondary structure near the endonucleolytic cleavage site downstream from the 5S rRNA coding region. We hypothesize that these duplexes are degraded by a dsRNA-specific ribonuclease in vivo, contributing to the 5S rRNA deficiency observed in rnr1. PMID:21148395

Impact of Sampling and Cellular Separation on Amino Acid Determinations in Drosophila Hemolymph.

PubMed

Cabay, Marissa R; Harris, Jasmine C; Shippy, Scott A

2018-04-03

The fruit fly is a frequently used model system with a high degree of human disease-related genetic homology. The quantitative chemical analysis of fruit fly tissues and hemolymph uniquely brings chemical signaling and compositional information to fly experimentation. The work here explores the impact of measured chemical content of hemolymph with three aspects of sample collection and preparation. Cellular content of hemolymph was quantitated and removed to determine hemolymph composition changes for seven primary amine analytes. Hemolymph sampling methods were adapted to determine differences in primary amine composition of hemolymph collected from the head, antenna, and abdomen. Also, three types of anesthesia were employed with hemolymph collection to quantitate effects on measured amino acid content. Cell content was found to be 45.4 ± 22.1 cells/nL of hemolymph collected from both adult and larvae flies. Cell-concentrated fractions of adult, but not larvae, hemolymph were found to have higher and more variable amine content. There were amino acid content differences found between all three areas indicating a robust method to characterize chemical markers from specific regions of a fly, and these appear related to physiological activity. Methods of anesthesia have an impact on hemolymph amino acid composition related to overall physiological impact to fly including higher amino acid content variability and oxygen deprivation effects. Together, these analyses identify potential complications with Drosophila hemolymph analysis and opportunities for future studies to relate hemolymph content with model physiological activity.

Impact of Air Pollutants on Oxidative Stress in Common Autophagy-Mediated Aging Diseases

PubMed Central

Numan, Mohamed Saber; Brown, Jacques P.; Michou, Laëtitia

2015-01-01

Atmospheric pollution-induced cellular oxidative stress is probably one of the pathogenic mechanisms involved in most of the common autophagy-mediated aging diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), Alzheimer’s, disease, as well as Paget’s disease of bone with or without frontotemporal dementia and inclusion body myopathy. Oxidative stress has serious damaging effects on the cellular contents: DNA, RNA, cellular proteins, and cellular organelles. Autophagy has a pivotal role in recycling these damaged non-functional organelles and misfolded or unfolded proteins. In this paper, we highlight, through a narrative review of the literature, that when autophagy processes are impaired during aging, in presence of cumulative air pollution-induced cellular oxidative stress and due to a direct effect on air pollutant, autophagy-mediated aging diseases may occur. PMID:25690002

Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.

PubMed

Madhaiyan, Munusamy; Alex, Tan Hian Hwee; Cho, Hayoung; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Whitman, William B; Ji, Lianghui

2017-12-01

Two yellow-pigmented isolates, S5-249 T and L9-754 T , originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249 T and L9-754 T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249 T and L9-754 T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937 T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249 T and L9-754 T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249 T and L9-754 T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937 T and the two type strains (S5-249 T and L9-754 T ) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249 T and L9-754 T ) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249 T =DSM 27345 T =KACC 17593 T ) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754 T =DSM 27347 T =KACC 17595 T ).

Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent.

PubMed

Zeng, Xiang; Zhang, Zhao; Li, Xi; Zhang, Xiaobo; Cao, Junwei; Jebbar, Mohamed; Alain, Karine; Shao, Zongze

2015-02-01

A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) ( = JCM 19466(T) = DSM 28033(T) = MCCC 1A06456(T)). © 2015 IUMS.

Hot topic: 16S rRNA gene sequencing reveals the microbiome of the virgin and pregnant bovine uterus.

PubMed

Moore, S G; Ericsson, A C; Poock, S E; Melendez, P; Lucy, M C

2017-06-01

We tested the hypothesis that the uterus of virgin heifers and pregnant cows possessed a resident microbiome by 16S rRNA gene sequencing of the virgin and pregnant bovine uterus. The endometrium of 10 virgin heifers in estrus and the amniotic fluid, placentome, intercotyledonary placenta, cervical lumen, and external cervix surface (control) of 5 pregnant cows were sampled using aseptic techniques. The DNA was extracted, the V4 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced using Illumina MiSeq technology (Illumina Inc., San Diego, CA). Operational taxonomic units (OTU) were generated from the sequences using Qiime v1.8 software, and taxonomy was assigned using the Greengenes database. The effect of tissue on the microbial composition within the pregnant uterus was tested using univariate (mixed model) and multivariate (permutational multivariate ANOVA) procedures. Amplicons of 16S rRNA gene were generated in all samples, supporting the contention that the uterus of virgin heifers and pregnant cows contained a microbiome. On average, 53, 199, 380, 382, 525, and 13,589 reads annotated as 16, 35, 43, 63, 48, and 176 OTU in the placentome, virgin endometrium, amniotic fluid, cervical lumen, intercotyledonary placenta, and external surface of the cervix, respectively, were generated. The 3 most abundant phyla in the uterus of the virgin heifers and pregnant cows were Firmicutes, Bacteroidetes, and Proteobacteria, and they accounted for approximately 40, 35, and 10% of the sequences, respectively. Phyla abundance was similar between the tissues of the pregnant uterus. Principal component analysis, one-way PERMANOVA analysis of the Bray-Curtis similarity index, and mixed model analysis of the Shannon diversity index and Chao1 index demonstrated that the microbiome of the control tissue (external surface of the cervix) was significantly different from that of the amniotic fluid, intercotyledonary placenta, and placentome tissues. Interestingly, many bacterial species associated with postpartum uterine disease (i.e., Trueperella spp., Acinetobacter spp., Fusobacteria spp., Proteus spp., Prevotella spp., and Peptostreptococcus spp.) were also present in the uterus of virgin heifers and of pregnant cows. The presence of 16S rRNA gene sequence reads in the samples from the current study suggests that the uterine microbiome is established by the time a female reaches reproductive maturity, and that pregnancies are established and maintained in the presence of a uterine microbiome. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Complete mitochondrial genome sequence of the Barbour's seahorse Hippocampus barbouri Jordan & Richardson, 1908 (Gasterosteiformes: Syngnathidae).

PubMed

Wang, Bo; Zhang, Yanhong; Zhang, Huixian; Lin, Qiang

2015-01-01

The complete mitochondrial genome sequence of the Barbour's seahorse Hippocampus barbouri was first determined in this paper. The total length of H. barbouri mitogenome is 16,526 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of the H. barbouri mitochondrial genome were similar to the typical vertebrates. The overall base composition of H. barbouri is 32.68% A, 29.75% T, 22.91% C and 14.66% G, with an AT content of 62.43%.

Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient.

PubMed

Leisner, J J; Vancanneyt, M; Goris, J; Christensen, H; Rusul, G

2000-01-01

Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions

NASA Astrophysics Data System (ADS)

Schopf, J. William; Kitajima, Kouki; Spicuzza, Michael J.; Kudryavtsev, Anatoliy B.; Valley, John W.

2018-01-01

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ˜3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ13C compositions to vary systematically taxon to taxon from ‑31‰ to ‑39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ13C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (‑27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (‑27.6‰), and those typical of modern prokaryotic phototrophs (‑25 ± 10‰). The SIMS data for the two highest δ13C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ13C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ13C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

Small Molecule Inhibitors of Staphylococcus aureus RnpA Alter Cellular mRNA Turnover, Exhibit Antimicrobial Activity, and Attenuate Pathogenesis

PubMed Central

Olson, Patrick D.; Kuechenmeister, Lisa J.; Anderson, Kelsi L.; Daily, Sonja; Beenken, Karen E.; Roux, Christelle M.; Reniere, Michelle L.; Lewis, Tami L.; Weiss, William J.; Pulse, Mark; Nguyen, Phung; Simecka, Jerry W.; Morrison, John M.; Sayood, Khalid; Asojo, Oluwatoyin A.; Smeltzer, Mark S.; Skaar, Eric P.; Dunman, Paul M.

2011-01-01

Methicillin-resistant Staphylococcus aureus is estimated to cause more U.S. deaths annually than HIV/AIDS. The emergence of hypervirulent and multidrug-resistant strains has further amplified public health concern and accentuated the need for new classes of antibiotics. RNA degradation is a required cellular process that could be exploited for novel antimicrobial drug development. However, such discovery efforts have been hindered because components of the Gram-positive RNA turnover machinery are incompletely defined. In the current study we found that the essential S. aureus protein, RnpA, catalyzes rRNA and mRNA digestion in vitro. Exploiting this activity, high through-put and secondary screening assays identified a small molecule inhibitor of RnpA-mediated in vitro RNA degradation. This agent was shown to limit cellular mRNA degradation and exhibited antimicrobial activity against predominant methicillin-resistant S. aureus (MRSA) lineages circulating throughout the U.S., vancomycin intermediate susceptible S. aureus (VISA), vancomycin resistant S. aureus (VRSA) and other Gram-positive bacterial pathogens with high RnpA amino acid conservation. We also found that this RnpA-inhibitor ameliorates disease in a systemic mouse infection model and has antimicrobial activity against biofilm-associated S. aureus. Taken together, these findings indicate that RnpA, either alone, as a component of the RNase P holoenzyme, and/or as a member of a more elaborate complex, may play a role in S. aureus RNA degradation and provide proof of principle for RNA catabolism-based antimicrobial therapy. PMID:21347352

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions.

PubMed

Schopf, J William; Kitajima, Kouki; Spicuzza, Michael J; Kudryavtsev, Anatoliy B; Valley, John W

2018-01-02

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ∼3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ 13 C compositions to vary systematically taxon to taxon from -31‰ to -39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ 13 C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (-27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (-27.6‰), and those typical of modern prokaryotic phototrophs (-25 ± 10‰). The SIMS data for the two highest δ 13 C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ 13 C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ 13 C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

Neisseria arctica sp. nov. isolated from nonviable eggs of greater white-fronted geese (Anser albifrons) in Arctic Alaska

USGS Publications Warehouse

Hansen, Cristina M.; Himschoot, Elizabeth; Hare, Rebekah F.; Meixell, Brandt W.; Van Hemert, Caroline R.; Hueffer, Karsten

2017-01-01

During the summers of 2013 and 2014, isolates of a novel Gram-negative coccus in the Neisseria genus were obtained from the contents of nonviable greater white-fronted goose (Anser albifrons) eggs on the Arctic Coastal Plain of Alaska. We used a polyphasic approach to determine whether these isolates represent a novel species. 16S rRNA gene sequences, 23S rRNA gene sequences, and chaperonin 60 gene sequences suggested that these Alaskan isolates are members of a distinct species that is most closely related to Neisseria canis, N. animaloris, and N. shayeganii. Analysis of the rplF gene additionally showed that our isolates are unique and most closely related to N. weaveri. Average nucleotide identity of the whole genome sequence of our type strain was between 71.5% and 74.6% compared to close relatives, further supporting designation as a novel species. Fatty acid methyl ester analysis showed a predominance of C14:0, C16:0, and C16:1ω7c fatty acids. Finally, biochemical characteristics distinguished our isolates from other Neisseria species. The name Neisseria arctica (type strain KH1503T = ATCC TSD-57T = DSM 103136T) is proposed.

Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei.

PubMed

Chu, Jiunn-Nan; Arun, A B; Chen, Wen-Ming; Chou, Jui-Hsing; Shen, Fo-Ting; Rekha, P D; Kämpfer, P; Young, Li-Sen; Lin, Shih-Yao; Young, Chiu-Chung

2010-09-01

A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117(T), was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C(18 : 1) ω 7c, C(19 : 0) cyclo ω 8c, C(16 : 0) and C(18 : 0) were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117(T) was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117(T) is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117(T) (=BCRC 17964(T) =CCM 7684(T)).

Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa.

PubMed

Xie, Cheng-Hui; Yokota, Akira

2006-04-01

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99.9 % 16S rRNA gene sequence similarity and greater than 70 % DNA-DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99.5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68.0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA-DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T = IAM 15283T = CCTCC AB205007T).

Glycomyces tarimensis sp. nov., an actinomycete isolated from a saline-alkali habitat.

PubMed

Lv, Ling-Ling; Zhang, Yue-Feng; Zhang, Li-Li

2015-05-01

A novel actinomycete strain, designated TRM 45387(T), was isolated from a saline-alkali soil in Xinjiang Province (40° 22' N 79° 08' E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45387(T) belonged to the genus Glycomyces and was closely related to Glycomyces arizonensis DSM 44726(T) (96.59% 16S rRNA gene sequence similarity). The G+C content of the DNA was 71.26 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and xylose, glucose, galactose, arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-10(H6). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of the evidence from this polyphasic study, a novel species, Glycomyces tarimensis sp. nov., is proposed. The type strain of Glycomyces tarimensis is TRM 45387(T) ( =CCTCC AA 2014007(T) =JCM 30184(T)). © 2015 Xinjiang Production & Construction Corps Key Laborartory of Protection and Utilization of Biological Resources in Tarim Basin.

Gaetbulibacter aestuarii sp. nov., isolated from shallow coastal seawater, and emended description of the genus Gaetbulibacter.

PubMed

Park, Seong Chan; Choe, Han Na; Baik, Keun Sik; Lee, Kang Hyun; Seong, Chi Nam

2012-01-01

A rod-shaped, yellow and strictly aerobic marine bacterium, designated KYW382(T), was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative and catalase- and oxidase-positive. The major fatty acids were iso-C(15:1) G, iso-C(15:0), iso-C(17:0) 3-OH, iso-C(15:0) 3-OH and anteiso-C(15:0). The DNA G+C content was 32.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW382(T) constituted an evolutionary lineage within the radiation enclosing the members of the genus Gaetbulibacter. The closest neighbour was Gaetbulibacter saemankumensis SMK-12(T) (96.1% 16S rRNA gene sequence similarity). A number of phenotypic characteristics distinguished strain KYW382(T) from the described members of the genus Gaetbulibacter. On the basis of the data presented in this study, strain KYW382(T) represents a novel species, for which the name Gaetbulibacter aestuarii sp. nov. is proposed. The type strain is KYW382(T) (=KCTC 23303(T) =JCM 17455(T)). An emended description of the genus Gaetbulibacter is also given.

Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge.

PubMed

Romanenko, Lyudmila A; Uchino, Masataka; Tanaka, Naoto; Frolova, Galina M; Mikhailov, Valery V

2008-02-01

An aerobic, Gram-negative bacterium, strain KMM 329(T), was isolated from a deep-sea sponge specimen from the Philippine Sea and subjected to a polyphasic taxonomic investigation. Comparative 16S rRNA gene sequence analysis showed that strain KMM 329(T) clustered with the species of the genus Lysobacter. The highest level of 16S rRNA gene sequence similarity (97.0 %) was found with respect to Lysobacter concretionis KCTC 12205(T); lower values (96.4-95.2 %) were obtained with respect to the other recognized Lysobacter species. The value for DNA-DNA relatedness between strain KMM 329(T) and L. concretionis KCTC 12205(T) was 47 %. Branched fatty acids 16 : 0 iso, 15 : 0 iso, 11 : 0 iso 3-OH and 17 : 1 iso were found to be predominant. Strain KMM 329(T) had a DNA G+C content of 69.0 mol%. On the basis of the phenotypic, chemotaxonomic, DNA-DNA hybridization and phylogenetic data, strain KMM 329(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter spongiicola sp. nov. is proposed. The type strain is KMM 329(T) (=NRIC 0728(T) =JCM 14760(T)).

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Nocardioides albertanoniae sp. nov., isolated from Roman catacombs.

PubMed

Alias-Villegas, Cynthia; Jurado, Valme; Laiz, Leonila; Miller, Ana Z; Saiz-Jimenez, Cesareo

2013-04-01

A Gram-reaction-positive, aerobic, non-spore-forming, rod- or coccoid-shaped, strain, CD40127(T), was isolated from a green biofilm covering the wall of the Domitilla Catacombs in Rome, Italy. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CD40127(T) belongs to the genus Nocardioides, closely related to Nocardioides luteus DSM 43366(T) and Nocardioides albus DSM 43109(T) with 98.86 % and 98.01 % similarity values, respectively. Strain CD40127(T) exhibited 16S rRNA gene sequence similarity values below 96.29 % with the rest of the species of the genus Nocardioides. The G+C content of the genomic DNA was 69.7 mol%. The predominant fatty acid was iso-C16 : 0 and the major menaquinone was MK-8(H4) in accordance with the phenotypes of other species of the genus Nocardioides. A polyphasic approach using physiological tests, fatty acid profiles, DNA base ratios and DNA-DNA hybridization showed that isolate CD40127(T) represents a novel species within the genus Nocardioides, for which the name Nocardioides albertanoniae is proposed. The type strain is CD40127(T) ( = DSM 25218(T) = CECT 8014(T)).

Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand.

PubMed

Hetzer, Adrian; Morgan, Hugh W; McDonald, Ian R; Daughney, Christopher J

2007-07-01

Surveys of Champagne Pool, one of New Zealand's largest terrestrial hot springs and rich in arsenic ions and compounds, have been restricted to geological and geochemical descriptions, and a few microbiological studies applying culture-independent methods. In the current investigation, a combination of culture and culture-independent approaches were chosen to determine microbial density and diversity in Champagne Pool. Recovered total DNA and adenosine 5'-triphosphate (ATP) content of spring water revealed relatively low values compared to other geothermal springs within New Zealand and are in good agreement with low cell numbers of 5.6 +/- 0.5 x 10(6) cells/ml obtained for Champagne Pool water samples by 4',6-diamidino-2-phenylindole (DAPI) staining. Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA (small-subunit ribosomal nucleic acid) gene clone library analyses of environmental DNA indicated the abundance of Sulfurihydrogenibium, Sulfolobus, and Thermofilum-like populations in Champagne Pool. From these results, media were selected to target the enrichment of hydrogen-oxidizing and sulfur-dependent microorganisms. Three isolates were successfully obtained having 16S rRNA gene sequences with similarities of approximately 98% to Thermoanaerobacter tengcongensis, 94% to Sulfurihydrogenibium azorense, and 99% to Thermococcus waiotapuensis, respectively.

Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.

PubMed

Kwong, Waldan K; Moran, Nancy A

2016-03-01

Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE PAGES

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.; ...

2016-09-29

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus.

PubMed

Hong, Yuan-Yuan; Ma, Yu-Chao; Zhou, Yu-Guang; Gao, Fei; Liu, Hong-Can; Chen, San-Feng

2009-11-01

A nitrogen-fixing bacterium, designated strain X19-5(T), was isolated from rhizosphere soil of Sonchus oleraceus. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain X19-5(T) was a member of the genus Paenibacillus. Strain X19-5(T) showed the highest 16S rRNA gene sequence similarity (98.8 %) with Paenibacillus graminis RSA19(T) and below 97 % similarity with other recognized members of the genus. The level of DNA-DNA relatedness between strain X19-5(T) and P. graminis RSA19(T) was 45.7 %. The DNA G+C content of strain X19-5(T) was 46.8 mol%. The major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain X19-5(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sonchi sp. nov. is proposed. The type strain is X19-5(T) (=CCBAU 83901(T)=LMG 24727(T)).

Complete mitochondrial genome of Taharana fasciana (Insecta, Hemiptera: Cicadellidae) and comparison with other Cicadellidae insects.

PubMed

Wang, Jiajia; Li, Hu; Dai, Renhuai

2017-12-01

Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A + T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A + T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG. Furthermore, we predicted the secondary structures of the rRNAs in T. fasciana. Six domains (domain III is absent in arthropods) and 41 helices were predicted for 16S rRNA, and 12S rRNA comprised three structural domains and 24 helices. Phylogenetic tree analysis confirmed that T. fasciana and other members of the Cicadellidae are clustered into a clade, and it identified the relationships among the subfamilies Deltocephalinae, Coelidiinae, Idiocerinae, Cicadellinae, and Typhlocybinae.

Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Senthilkumar, Murugaiyan; Lee, Jung-Sook; Lee, Keun-Chul

2012-01-01

A pink, aerobic, facultatively methylotrophic, motile, Gram-negative rod, designated Gh-105(T), was isolated from the phyllosphere of cotton from Coimbatore (Tamilnadu, India). 16S rRNA gene sequence analysis showed clearly that the isolate belonged to the Methylobacterium cluster. Strain Gh-105(T) was most closely related to Methylobacterium adhaesivum AR27(T) (99% 16S rRNA gene sequence similarity) and Methylobacterium iners 5317S-33(T) (97.5%). The isolate grew with C(1) compounds such as methanol and dichloromethane, but not with formaldehyde, formate, methylamine, trimethylamine or methane, as sole carbon sources and carried mxaF, which encodes methanol dehydrogenase and supports methylotrophic metabolism. The major fatty acid was C(18:1)ω7c and the G+C content of the genomic DNA was 64.2 mol%. Physiological and biochemical data and DNA-DNA relatedness with M. adhaesivum KACC 12195(T) and M. iners KACC 11765(T) revealed clear phenotypic and genotypic differences. For this reason, we propose that strain Gh-105(T) (=CCM 7572(T) =NRRL B-51692(T)) represents the type strain of a novel species, with the name Methylobacterium gossipiicola sp. nov.

The nucleotide sequence of the entire ribosomal DNA operon and the structure of the large subunit rRNA of Giardia muris.

PubMed

van Keulen, H; Gutell, R R; Campbell, S R; Erlandsen, S L; Jarroll, E L

1992-10-01

The total nucleotide sequence of the rDNA of Giardia muris, an intestinal protozoan parasite of rodents, has been determined. The repeat unit is 7668 basepairs (bp) in size and consists of a spacer of 3314 bp, a small-subunit rRNA (SSU-rRNA) gene of 1429, and a large-subunit rRNA (LSU-rRNA) gene of 2698 bp. The spacer contains long direct repeats and is heterogeneous in size. The LSU-rRNA of G. muris was compared to that of the human intestinal parasite Giardia duodenalis, to the bird parasite Giardia ardeae, and to that of Escherichia coli. The LSU-rRNA has a size comparable to the 23S rRNA of E. coli but shows structural features typical for eukaryotes. Some variable regions are typically small and account for the overall smaller size of this rRNA. The structure of the G. muris LSU-rRNA is similar to that of the other Giardia rRNA, but each rRNA has characteristic features residing in a number of variable regions.

Exploration of RNA structure spaces

NASA Technical Reports Server (NTRS)

Fox, G. E.

1991-01-01

In order to understand the structure of real structure spaces, we are studying the 5S rRNA structure space experimentally. A plasmid containing a synthetic 5S rRNA gene, two rRNA promoters, and transcription terminators has been assembled. Assays are conducted to determine if the foreign 5S rRNA is expressed, and to see whether or not it is incorporated into ribosomes. Evolutionary competition is used to determine the relative fitness of strains containing the foreign 5S rRNA and a control 5S rRNA. By using site directed mutagenesis, a number of mutants can be made in order to study the boundaries of the structure space and how sharply defined they are. By making similar studies in the vicinity of structure space, it will be possible to determine how homogeneous the 5S rRNA structure space is. Useable experimental protocols have been developed, and a number of mutants have already been studied. Initial results suggest an explanation of why single stranded regions of the RNA are less subject to mutation than double stranded regions.

rrndb: the Ribosomal RNA Operon Copy Number Database

PubMed Central

Klappenbach, Joel A.; Saxman, Paul R.; Cole, James R.; Schmidt, Thomas M.

2001-01-01

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu. PMID:11125085

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

PubMed Central

Su, Aiguo; Geng, Jianing; Grover, Corrinne E.; Hu, Songnian; Hua, Jinping

2013-01-01

Background Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. Methodology/Principal Findings We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. Conclusion The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species. PMID:23940520

The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

PubMed

Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing; Grover, Corrinne E; Hu, Songnian; Hua, Jinping

2013-01-01

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

Identification of "Haematobacter," a new genus of aerobic Gram-negative rods isolated from clinical specimens, and reclassification of Rhodobacter massiliensis as "Haematobacter massiliensis comb. nov.".

PubMed

Helsel, Leta O; Hollis, Dannie; Steigerwalt, Arnold G; Morey, Roger E; Jordan, Jean; Aye, Tin; Radosevic, Jon; Jannat-Khah, Deanna; Thiry, Dorothy; Lonsway, David R; Patel, Jean B; Daneshvar, Maryam I; Levett, Paul N

2007-04-01

Twelve strains of gram-negative, nonfermenting rods recovered mainly from septicemic patients were studied using conventional and molecular methods. The phenotypic profiles of these strains most closely resembled Psychrobacter phenylpyruvicus. They produced catalase, oxidase, urease, and H(2)S (lead acetate paper) but did not produce indole, reduce nitrate or nitrite, or hydrolyze gelatin or esculin. No acid production was observed in a King's oxidation-fermentation base containing d-glucose, d-xylose, d-mannitol, sucrose, lactose, or maltose. All strains were nonmotile and nonpigmented. Most strains produced green discoloration on blood agar. All strains grew at 25 degrees C and 35 degrees C and most grew on MacConkey agar. They shared a common cellular fatty acid (CFA) profile characterized by large amounts (56% to 90%) of 18:1omega7c and the presence of 3-OH-10:0, 16:1omega7c, 16:0, and 19:0cycomega8c that overall was most similar to that of Rhodobacter species but was quite distinct from that of P. phenylpyruvicus. The MICs for most beta-lactams, fluoroquinolones, aminoglycosides, and carbapenems were low. MICs for aztreonam and piperacillin were higher, with MICs for some strains of > 64 mg/liter and > 128 mg/liter, respectively. Polyphasic analysis of these strains, including morphological, biochemical, CFA composition, DNA-DNA hybridization, 16S rRNA gene sequencing, and percent guanine-plus-cytosine (G+C) content analysis, demonstrated that these strains and Rhodobacter massiliensis represent a new genus, "Haematobacter" (proposed name), with the species H. missouriensis (type strain H1892(T) = CCUG 52307(T) = CIP 109176(T)) and H. massiliensis comb. nov. (type strain Framboise(T) = CCUG 47968(T) = CIP 107725(T)) and an unnamed genomospecies.

Ichthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum 'Bacteroidetes', isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.

PubMed

Takano, Tomokazu; Matsuyama, Tomomasa; Sakai, Takamitsu; Nakamura, Yoji; Kamaishi, Takashi; Nakayasu, Chihaya; Kondo, Hidehiro; Hirono, Ikuo; Fukuda, Yutaka; Sorimachi, Minoru; Iida, Takaji

2016-02-01

A novel Gram-stain-negative, rod-shaped (0.3 × 4-6 μm), non-flagellated, aerobic strain with gliding motility, designated JBKA-6T, was isolated in 1991 from a yellowtail fish, Seriola quinqueradiata, showing symptoms of bacterial haemolytic jaundice. 16S rRNA gene sequence analysis showed that strain JBKA-6T was related most closely to members of the family Flavobacteriaceae in the phylum 'Bacteroidetes'. Furthermore, based on gyrB gene sequence analysis, JBKA-6T was classified into a single clade within the order Flavobacteriales, which was distinct from the known clades of the families Flavobacteriaceae, Blattabacteriaceae and Cryomorphaceae. The predominant isoprenoid quinone was identified as MK-6 (97.9 %), and the major cellular fatty acids (>10 %) were C14 : 0 and iso-C15 : 0. The main polar lipids were phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminophospholipids and two unidentified polar lipids. The DNA G+C content of JBKA-6T, as derived from its whole genome, was 33.4 mol%. The distinct phylogenetic position and phenotypic traits of strain JBKA-6T distinguish it from all other described species of the phylum 'Bacteroidetes', and therefore it was concluded that strain JBKA-6T represents a new member of the phylum 'Bacteroidetes', and the name Ichthyobacterium seriolicida gen. nov., sp. nov. is proposed. The type strain of Ichthyobacterium seriolicida is JBKA-6T ( = ATCC BAA-2465T = JCM 18228T). We also propose that Icthyobacterium gen. nov. is the type genus of a novel family, Ichthyobacteriaceae fam. nov.

Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae.

PubMed

Zhang, Wei-Yan; Fang, Ming-Xu; Zhang, Wen-Wu; Xiao, Chuan; Zhang, Xin-Qi; Yu, Zhi-Ping; Zhu, Xu-Fen; Wu, Min

2013-06-01

A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8-0.9 × 1.3-1.9 µm and the cells elongated to 10-25 µm when cultivated at high temperatures. Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 5.5-8.5 (optimum 7.0-7.5) and 0-2% (optimum 0.5%) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (94.6-95.6% similarities), Giesbergeria (94.9-95.6%), Acidovorax (94.8-95.4%), Brachymonas (94.1-95.2%) and Macromonas (95.1%). Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 1.10977(T)=JCM 17803(T)).

Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov.

PubMed

Dalmastri, Claudia; Gastaldo, Luciano; Marcone, Giorgia Letizia; Binda, Elisa; Congiu, Terenzio; Marinelli, Flavia

2016-02-01

Strain ATCC 39727, which produces the antibiotic A40926 (the natural precursor of the antibiotic dalbavancin), was isolated from a soil sample collected in India, and it was originally classified as a member of the genus Actinomadura on the base of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicates that the strain forms a distinct clade within the genus Nonomuraea, and it is most closely related to Nonomuraea angiospora DSM 43173T (98.72 % similarity) and Nonomuraea jabiensis A4036T (98.69 %). The strain forms an extensively branched substrate mycelium and aerial hyphae that form spiral chains of spores with ridged surfaces. The cell wall contains meso-diaminopimelic acid and the whole-cell sugars are glucose, ribose, galactose, mannose and madurose (madurose as the diagnostic sugar). The N-acyl type of muramic acid is acetyl. The predominant menaquinone is MK-9(H4), with minor amounts of MK-9(H2), MK-9(H6) and MK-9(H0). The polar-lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylinositol and a series of uncharacterized phospholipids, glycolipids and phosphoglycolipids. The major cellular fatty acids are iso-C16 : 0 and 10-methyl C17 : 0. The genomic DNA G+C content is 71.2 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA-DNA relatedness between strain ATCC 39727 and closely related type strains, clearly demonstrated that strain ATCC 39727 represents a novel species of the genus Nonomuraea, for which the name Nonomuraea gerenzanensis sp. nov. is proposed. The type strain is ATCC 39727T ( = DSM 100948T).

Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil.

PubMed

Zhang, Lei; Shen, Xihui; Liu, Yingbao; Li, Shiqing

2013-05-01

A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10(T), was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30-37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10(T) was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311(T) (90.2 % sequence similarity), Marivirga sericea LMG 13021(T) (89.2 %), Cesiribacter andamanensis AMV16(T) (89.1 %) and Marivirga tractuosa DSM 4126(T) (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10(T) should be classified as a novel species of a new genus in the family Flammeovirgaceae, for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10(T) ( = CCTCC AB 208222(T) = KCTC 23983(T)).

Aquimarina agarivorans sp. nov., a genome-sequenced member of the class Flavobacteriia isolated from Gelidium amansii.

PubMed

Zhou, Yan-Xia; Wang, Chao; Du, Zong-Jun; Chen, Guan-Jun

2015-08-01

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped, agar-digesting bacterial strain, designated HQM9T, was isolated from the surface of the marine red alga Gelidium amansii collected from the intertidal zone of Weihai, China. Cells of HQM9T were 3.0-4.0 μm long and 0.2-0.3 μm wide and lacked flagella. The new isolate grew optimally at 28-30 °C, at pH 7.0-7.5, and in the presence of 2.5-3.0% NaCl. The predominant cellular fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The sole menaquinone was MK-6. The DNA G+C content was 33 mol%. The major polar lipids were comprised of phosphatidylethanolamine and four unknown polar lipids. Based on the 16S rRNA gene sequence, the closest relative was Aquimarina agarilytica ZC1T with 97.16% sequence similarity, with which strain HQM9T formed a distinct cluster belonging to the genus Aquimarina in a phylogenetic tree. Moreover, average nucleotide identity and estimated DNA-DNA hybridization values between strains HQM9T and ZC1T were 78.7% and 12.50 ± 2.95%, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain HQM9T represents the type strain of a novel species within the genus Aquimarina in the family Flavobacteriaceae, phylum Bacteroidetes, for which the name Aquimarina agarivorans sp. nov. is proposed. The type strain is HQM9T ( = ATCC BAA-2612T = CICC 10835T).

Mesonia hippocampi sp. nov., isolated from the brood pouch of a diseased Barbour's Seahorse (Hippocampus barbouri).

PubMed

Kolberg, Judy; Busse, Hans-Jürgen; Wilke, Thomas; Schubert, Patrick; Kämpfer, Peter; Glaeser, Stefanie P

2015-07-01

An orange-pigmented, Gram-staining-negative, rod-shaped bacterium, designated 96_Hippo_TS_3/13(T) was isolated from the brood pouch of a diseased seahorse male of the species Hippocampus barbouri from the animal facility of the University of Giessen, Germany. Phylogenetic analyses based on the nearly full-length 16S rRNA gene sequence placed strain 96_Hippo_TS_3/13(T) into the monophyletic cluster of the genus Mesonia within the family Flavobacteriaceae. However, the strain shared only 92.2-93.8% sequence similarity to type strains of species of the genus Mesonia, with highest sequence similarity to the type strain of Mesonia aquimarina. Cellular fatty acid analysis showed a Mesonia-typical fatty acid profile including several branched and hydroxyl fatty acids with highest amounts of iso-C15 : 0 (40.9%) followed by iso-C17 : 0 3-OH (14.8%). In the polyamine pattern, sym-homospermidine was predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-6. The only identified compound in the polar lipid profile was phosphatidylethanolamine present in major amounts. Additionally, major amounts of an unidentified aminolipid and two unidentified lipids not containing a phosphate group, an amino group or a sugar residue were detected. The genomic G+C content of strain 96_Hippo_TS_3/13(T) was 30 mol%. Based on genotypic, chemotaxonomic and physiological characterizations we propose a novel species of the genus Mesonia, Mesonia hippocampi sp. nov., with strain 96_Hippo_TS_3/13(T) ( = CIP 110839T =  LMG 28572(T) = CCM 8557(T)) as the type strain. An emended description of the genus Mesonia is also provided.

Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov., soil myxobacteria, and emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceae.

PubMed

Awal, Ram Prasad; Garcia, Ronald; Gemperlein, Katja; Wink, Joachim; Kunwar, Bikram; Parajuli, Niranjan; Müller, Rolf

2017-05-01

Bacterial strains MCy10943T and MCy10944T were isolated in 2014 from dried Nepalese soil samples collected in 2013 from Phukot, Kalikot, Western Nepal, and Godawari, Lalitpur, Central Nepal. The novel organisms showed typical myxobacterial growth characteristics, which include swarming colony and fruiting body formation on solid surfaces, and a predatory ability to lyse micro-organisms. The strains were aerobic, mesophilic, chemoheterotrophic and showed resistance to various antibiotics. The major cellular fatty acids common to both organisms were C17 : 0 2-OH, iso-C15 : 0, C16 : 1 and iso-C17 : 0. The G+C content of the genomic DNA was 72-75 mol%. Phylogenetic analysis showed that the strains belong to the family Cystobacteraceae, suborder Cystobacterineae, order Myxococcales. The 16S rRNA gene sequences of both strains showed 97-98 % similarity to Archangium gephyra DSM 2261T andCystobacter violaceus DSM 14727T, and 96.7-97 % to Cystobacter fuscus DSM 2262T and Angiococcus disciformis DSM 52716T. Polyphasic taxonomic characterization suggested that strains MCy10943T and MCy10944T represent two distinct species of a new genus, for which the names Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov. are proposed. The type strain of Vitiosangium cumulatum is MCy10943T (=DSM 102952T=NCCB 100600T) while that for Vitiosangium subalbum is MCy10944T (=DSM 102953T=NCCB 100601T). In addition, emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceaeare provided.

Characterization of Marinomonas algicida sp. nov., a novel algicidal marine bacterium isolated from seawater.

PubMed

Kristyanto, Sylvia; Chaudhary, Dhiraj Kumar; Lee, Sang-Seob; Kim, Jaisoo

2017-11-01

A novel Marinomonas-like, aerobic, Gram-reaction-negative, moderately halophilic, acidophilic, motile by a single polar flagellum, non-spore-forming, rod-shaped bacterium that showed algalytic activity, designated strain Yeongu 1-4 T , was isolated from surface seawater of Geoje Island in the South Sea, Republic of Korea. The strain was oxidase-negative and weakly positive for catalase. Growth of this bacterium was observed at temperatures from 4 to 42 °C, at salinities from 0 to 12 % and at pH from 4.5 to 9.0, and it was not able to degrade starch, gelatin, casein or Tween 80. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Yeongu 1-4 T was related most closely to Marinomonas spartinae SMJ19 T with similarity of 99.3 %. However, levels of DNA-DNA relatedness between strain Yeongu 1-4 T and the most closely related species were lower than 70 %, confirming that they represent distinct genomic species. The genomic DNA G+C content of strain Yeongu 1-4 T was 44.2 mol%. The organism used Q-8 as the predominant respiratory quinone, and C16 : 1ω7c, C18 : 1ω7c and C16 : 0 as major cellular fatty acids. Based on data from this polyphasic taxonomic study, strain Yeongu 1-4 T belongs to a novel species of the genus Marinomonas, within the family Oceanospirillaceae, for which the name Marinomonas algicida is proposed. The type strain is Yeongu 1-4 T (=KEMB 9005-327 T =MCCC 1K00609 T ).

Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis.

PubMed

Wen, Zhi-Qiang; Chen, Bingzhi; Li, Xiao; Li, Bing-Bing; Li, Cheng-Huan; Huang, Qing-Hua; Zhang, Qi-Hui; Dai, Wei-Hao; Jiang, Yu-Ji

2016-12-01

A novel actinomycete strain, designated Js-1T, was isolated from Tremella fuciformis collected from Gutian, Fujian Province, in southeastern China. The taxonomic status of this strain was determined by a polyphasic approach, which demonstrated that the novel strain was a member of the genus Streptomyces. The cell walls of this strain were found to contain ll-diaminopimelic acid, muramic acid and glycine. An analysis of whole-cell hydrolysates revealed that no characteristic sugar was present. The key identified menaquinones were MK-9 (H6) and MK-9 (H8), while the diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmethylethanolamine and phosphatidylglycerol. The main cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. An analysis of an almost complete 16S rRNA gene sequence showed that the strain shared the highest levels of sequence similarity with Streptomyces sannanensisKC-7038T (97.87 %), Streptomyces hebeiensis YIM 001T (97.84 %), Streptomyces pathocidini NBRC 13812T (97.80 %), Streptomyces cocklensis BK168T (97.25 %), Streptomyces coerulescens NBRC 12758T (97.12 %), Streptomyces aurantiogriseus NBRC 12842T (97.06 %) and Streptomyces rimosussubsp. rimosus ATCC 10970T (97.04 %). The DNA G+C content of the genomic DNA of strain Js-1T was 70.1 mol%. Furthermore, DNA-DNA hybridization tests revealed that the relatedness values between strain Js-1T and the most closely related species ranged from 15.10 to 47.20 %. Based on its phenotypic and genotypic characteristics, strain Js-1T (=CCTCC M 2011365T=JCM 30846T) is considered to represent a novel species within the genus Streptomyces, which we classified as Streptomycestremellae sp. nov.

Lactobacillus ixorae sp. nov., isolated from a flower (West-Indian jasmine).

PubMed

Techo, Sujitra; Miyashita, Mika; Shibata, Chiyo; Tanaka, Naoto; Wisetkhan, Preeyarach; Visessanguan, Wonnop; Tanasupawat, Somboon

2016-12-01

A Gram-stain-positive, lactic acid bacterium, strain Ru20-1T, was isolated from a flower (West-Indian jasmine) collected from Kalasin province, Thailand. A polyphasic approach was used to determine the taxonomic position of this strain. Studies of morphological and biochemical characteristics revealed that strain Ru20-1T belonged to the genus Lactobacillus. The strain was heterofermentative, non-spore-forming and rod-shaped. It produced dl-lactic acid. Based on 16S rRNA gene sequence similarity, this strain was closely related to Lactobacillus lindneri LMG 14528T (96.8 %), Lactobacillus sanfranciscensis NRIC 1548T (95.4 %) and Lactobacillus florum NRIC 0771T (95.2 %), respectively. In addition, the pheS gene sequence of strain Ru20-1T was closely related to those of L. sanfranciscensis NRIC 1548T (92.0 %), L. lindneri LMG 14528T (89.0 %) and L. florum NRIC 0771T(85.0 %). Phylogenetic analysis indicated that strain Ru20-1T was clearly separated from closely related species of the genus Lactobacillus. The DNA G+C content of strain Ru20-1T was 47.8 mol %. The cell-wall peptidoglycan type was l-Lys-d-Asp. The major cellular fatty acids were C18 : 1ω9c, C20 : 0, C20 : 1ω9c and summed feature 7 (unknown 18.846 and/or C19 : 1ω6c and/or C19 : 0 cyclo). On the basis of the data provided, strain Ru20-1T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus ixorae sp. nov. is proposed. The type strain is Ru20-1T (=LMG 29008T=NBRC 111239T=PCU 346T=TISTR 2381T).

Bacteria associated with cysts of the soybean cyst nematode (Heterodera glycines).

PubMed

Nour, Sarah M; Lawrence, John R; Zhu, Hong; Swerhone, George D W; Welsh, Martha; Welacky, Tom W; Topp, Edward

2003-01-01

The soybean cyst nematode (SCN), Heterodera glycines, causes economically significant damage to soybeans (Glycine max) in many parts of the world. The cysts of this nematode can remain quiescent in soils for many years as a reservoir of infection for future crops. To investigate bacterial communities associated with SCN cysts, cysts were obtained from eight SCN-infested farms in southern Ontario, Canada, and analyzed by culture-dependent and -independent means. Confocal laser scanning microscopy observations of cyst contents revealed a microbial flora located on the cyst exterior, within a polymer plug region and within the cyst. Microscopic counts using 5-(4,6-dichlorotriazine-2-yl)aminofluorescein staining and in situ hybridization (EUB 338) indicated that the cysts contained (2.6 +/- 0.5) x 10(5) bacteria (mean +/- standard deviation) with various cellular morphologies. Filamentous fungi were also observed. Live-dead staining indicated that the majority of cyst bacteria were viable. The probe Nile red also bound to the interior polymer, indicating that it is lipid rich in nature. Bacterial community profiles determined by denaturing gradient gel electrophoresis analysis were simple in composition. Bands shared by all eight samples included the actinobacterium genera Actinomadura and STREPTOMYCES: A collection of 290 bacteria were obtained by plating macerated surface-sterilized cysts onto nutrient broth yeast extract agar or on actinomycete medium. These were clustered into groups of siblings by repetitive extragenic palindromic PCR fingerprinting, and representative isolates were tentatively identified on the basis of 16S rRNA gene sequence. Thirty phylotypes were detected, with the collection dominated by Lysobacter and Variovorax spp. This study has revealed the cysts of this important plant pathogen to be rich in a variety of bacteria, some of which could presumably play a role in the ecology of SCN or have potential as biocontrol agents.

Differential Responses of the Antioxidant System of Ametryn and Clomazone Tolerant Bacteria

PubMed Central

Peters, Leila Priscila; Carvalho, Giselle; Martins, Paula Fabiane; Dourado, Manuella Nóbrega; Vilhena, Milca Bartz; Pileggi, Marcos; Azevedo, Ricardo Antunes

2014-01-01

The herbicides ametryn and clomazone are widely used in sugarcane cultivation, and following microbial degradation are considered as soil and water contaminants. The exposure of microorganisms to pesticides can result in oxidative damage due to an increase in the production of reactive oxygen species (ROS). This study investigated the response of the antioxidant systems of two bacterial strains tolerant to the herbicides ametryn and clomazone. Bacteria were isolated from soil with a long history of ametryn and clomazone application. Comparative analyses based on 16S rRNA gene sequences revealed that strain CC07 is phylogenetically related to Pseudomonas aeruginosa and strain 4C07 to P. fulva. The two bacterial strains were grown for 14 h in the presence of separate and combined herbicides. Lipid peroxidation, reduced glutathione content (GSH) and antioxidant enzymes activities were evaluated. The overall results indicated that strain 4C07 formed an efficient mechanism to maintain the cellular redox balance by producing reactive oxygen species (ROS) and subsequently scavenging ROS in the presence of the herbicides. The growth of bacterium strain 4C07 was inhibited in the presence of clomazone alone, or in combination with ametryn, but increased glutathione reductase (GR) and glutathione S-transferase (GST) activities, and a higher GSH concentration were detected. Meanwhile, reduced superoxide dismutase (SOD), catalase (CAT) and GST activities and a lower concentration of GSH were detected in the bacterium strain CC07, which was able to achieve better growth in the presence of the herbicides. The results suggest that the two bacterial strains tolerate the ametryn and clomazone herbicides with distinctly different responses of the antioxidant systems. PMID:25380132

Soortia roseihalophila gen. nov., sp. nov., a new taxon in the order Balneolales isolated from a travertine spring, and description of Soortiaceae fam. nov.

PubMed

Amoozegar, Mohammad Ali; Khansha, Javad; Mehrshad, Maliheh; Shahzadeh Fazeli, Seyed Abolhassan; Ramezani, Mohaddaseh; de la Haba, Rafael R; Sánchez-Porro, Cristina; Ventosa, Antonio

2017-01-01

A novel Gram-stain-negative, slightly halophilic, motile, curved rod with a horseshoe shape, designated strain Bsw-2bT, was isolated from Badab-Soort travertine spring in Iran. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Bsw-2bT belongs to the order Balneolales, showing 84.6 % sequence similarity to Gracilimonastropica DSM 19535T and 84.4 % and 83.9 % sequence similarity to Gracilimonas rosea CL-KR2T and Balneola vulgaris DSM 17893T, respectively. In addition, phenotypic and physiological features could clearly differentiate strain Bsw-2bT from species of the most closely related genera, Gracilimonas, Balneola, Aliifodinibius and Fodinibius. The strain was able to grow with 1-3 % (w/v) (optimum at 2 %) NaCl, at temperatures of 28-34 °C (optimum at 30 °C) and between pH 6.0 and 8.0 (optimum at pH 7.0). The major cellular fatty acids of strain Bsw-2bT were iso-C15 : 0, iso-C13 : 0 and iso-C14 : 0. The polar lipid profile of strain Bsw-2bT was composed predominantly of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid and four unknown phospholipids. The DNA G+C content was 40.5 mol%. Based on the evidence from the polyphasic study, strain Bsw-2bT represents a novel species in a novel genus within a new family, for which the name Soortia roseihalophila gen. nov., sp. nov. is proposed, within the new family Soortiaceae fam. nov. The type strain is strain Bsw-2bT (=IBRC-M 10915T=LMG 28547T).

Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.

PubMed

Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

2013-02-01

A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16 : 0) (34.2 %), iso-C(16 : 0) (18 %), C(18 : 0) (12.8 %) and iso-C(17 : 0) (11.1 %). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2 % sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) ( = DSM 22653(T) = VKM B-2685(T)).

Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae).

PubMed

Bang, Byung-Ho; Rhee, Moon-Soo; Chang, Dong-Ho; Park, Doo-Sang; Kim, Byoung-Chan

2015-02-01

A novel, Gram-stain positive, facultative anaerobic, non-motile and straight to curve rod shaped bacterium, strain LV19(T) was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus, which was collected from Yeong-dong, Chuncheongbuk-do, South Korea. The colonies of the new isolate were convex, circular, cream white in color and 1-2 mm in diameter after 3 days incubation on Tryptic Soy Agar at 37 °C. Based on the 16S rRNA gene sequence similarity, the new isolate was most closely related to Erysipelothrix inopinata MF-EP02(T), E. rhusiopathiae ATCC 19414 (T) and E. tonsillarum T-305(T) (94.8, 93.8 and 93.7 % similarity, respectively). Strain LV19(T) grew optimally at 37 °C, at pH 8.0 and in the presence of 0.5 % (w/v) NaCl. Oxidase activity and catalase activity were negative. The major cellular fatty acids (>10 %) were C18:2 cis-9,12 (28.9 %), C18:1 cis-9 (22.3 %), C16:0 (22.2 %) and C18:0 (18.5 %). The cell-wall hydrolysates contained ribose as a major sugar. Major polar lipids were phosphatidylglycerol and three unidentified glycolipids. No quinone was detected. The G+C content of the genomic DNA was 36.3 mol%. The levels of DNA-DNA relatedness between strain LV19(T) and all the reference strains were less than 20 %. On the basis of polyphasic evidence from this study, the isolate is considered to represent a novel species of the genus Erysipelothrix, for which the name Erysipelothrix larvae sp. nov. is proposed; the type strain is LV19(T) (=KCTC 33523(T) = DSM 28480(T)).

Saccharomonospora piscinae sp. nov., a novel actinobacterium from fishpond sediment in Taiwan.

PubMed

Tseng, Min; Chiang, Wan-Ping; Liao, Hsuen-Chun; Hsieh, Sung-Yuan; Yuan, Gao-Fung

2018-05-01

Strain 06168H-1 T was isolated from a fishpond sediment sample collected from the southern area of Taiwan, and a polyphasic approach was used to determine its taxonomic position. The isolate grew between 20-40 °C and 0-8 % (w/v) NaCl. It produced branched and unfragmented substrate mycelia. Short spore chains (3-10 spores per chain) formed on branched aerial mycelia. The spore chains contained non-motile, smooth-surfaced, oval spores. Galactose, arabinose and ribose were the whole-cell sugars and meso-diaminopimelic acid was present in its peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, hydroxyphosphati dylethanolamine and a ninhydrin-positive phosphoglycolipid. The predominant menaquinone was MK-9(H4) and minor components were MK-8(H4) and MK-9(H6). Mycolic acids were not detected. The major cellular fatty acids were iso-C16 : 0 and C17 : 1ω6c and C17 : 0ω8c. The DNA G+C content of the strain was 70.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed this strain clustered with the members of the genus Saccharomonospora and was closely related to Saccharomonospora xinjiangensis, Saccharomonospora azurea and Saccharomonosporacyanea. The levels of similarity between this strain and the closely related species were: Sxinjiangensis BCRC16887 T , 98.34 %; S. azurea BCRC 16220 T , 98.27 %; and S. cyanea BCRC 16886 T , 97.99 %. Based on phylogenetic characteristics, strain 06168H-1 T represents a novel species of the genus Saccharomonospora. We thus propose the name Saccharomonospora piscinae sp. nov. for this novel strain, with strain 06168H-1 T (=BCRC 16893 T =KCTC 19743 T ) as the type strain.

Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

PubMed

Downes, Julia; Dewhirst, Floyd E; Tanner, Anne C R; Wade, William G

2013-04-01

Five strains of anaerobic, gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae, and the most closely related species was Prevotella tannerae. P. tannerae and the novel taxon are deeply branched from the genus Prevotella, with sequence identities to the type strain of the type species of Prevotella, Prevotella melaninogenica, of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12(T) ( = DSM 22548(T)  = CCUG 58091(T)) and the type strain of Alloprevotella tannerae is ATCC 51259(T)  = CCUG 34292(T)  = CIP 104476(T)  = NCTC 13073(T). Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.

Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

PubMed Central

Downes, Julia; Dewhirst, Floyd E.; Tanner, Anne C. R.

2013-01-01

Five strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae, and the most closely related species was Prevotella tannerae. P. tannerae and the novel taxon are deeply branched from the genus Prevotella, with sequence identities to the type strain of the type species of Prevotella, Prevotella melaninogenica, of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12T ( = DSM 22548T  = CCUG 58091T) and the type strain of Alloprevotella tannerae is ATCC 51259T  = CCUG 34292T  = CIP 104476T  = NCTC 13073T. Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%. PMID:22753527

Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).

PubMed

Tanasupawat, Somboon; Takehana, Toshihiko; Yoshida, Shosuke; Hiraga, Kazumi; Oda, Kohei

2016-08-01

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Fusibacter bizertensis sp. nov., isolated from a corroded kerosene storage tank.

PubMed

Smii, Latifa; Ben Hania, Wajdi; Cayol, Jean-Luc; Joseph, Manon; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

2015-01-01

Strain LTF Kr01(T), a novel mesophilic, anaerobic, halotolerant, rod-shaped bacterium, was isolated from a drain at the bottom of a corroded kerosene storage tank of the Société Tunisienne des Industries de Raffinage (STIR), Bizerte, northern Tunisia. Cells were Gram-positive-staining rods, occurred singly or in pairs, and were motile by one lateral flagellum. Strain LTF Kr01(T) grew at temperatures between 15 and 40 °C (optimum 30 °C), between pH 5.5 and 8.2 (optimum pH 7.2) and at NaCl concentrations between 0 and 50 g l(-1) (optimum 5 g l(-1)). It reduced thiosulfate and elemental sulfur into sulfide, but did not reduce sulfate or sulfite. It utilized a wide range of carbohydrates (cellobiose, d-glucose, d-fructose, d-mannitol, d-ribose, sucrose, d-xylose, maltose, d-galactose, starch and trehalose) and produced acetate, CO2 and H2 as end products from glucose fermentation. The DNA G+C content was 37.4 mol%. The predominant cellular fatty acids were C14:0 and C16:0. Phylogenetic analysis of the 16S rRNA gene sequence suggested that Fusibacter tunisiensis was the closest relative of strain LTF Kr01(T) (gene sequence similarity of 94.6%). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain LTF Kr01(T) is proposed to represent a novel species of the genus Fusibacter, order Clostridiales, for which the name Fusibacter bizertensis sp. nov. is proposed. The type strain is LTF Kr01(T) ( = DSM 28034(T) = JCM 19376(T)). © 2015 IUMS.

Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy.

PubMed

Poli, Annarita; Romano, Ida; Mastascusa, Vincenza; Buono, Lorena; Orlando, Pierangelo; Nicolaus, Barbara; Leone, Luigi; Hong, Kar Wai; Chan, Kok-Gan; Goh, Kian Mau; Pascual, Javier

2018-07-01

Strain Corallo1 T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1 T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1 T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1 T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1 T . A draft genome sequence of strain Corallo1 T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1 T are C 16:1 , n-C 16:0 and C 18:1 , and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1 T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1 T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1 T (= DSM 27495 T  = CIP 110630 T ).

Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces.

PubMed

Sakamoto, Mitsuo; Iino, Takao; Yuki, Masahiro; Ohkuma, Moriya

2018-06-01

An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22 T , was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22 T formed a monophyletic cluster with species in the genera Pseudoflavonifractor and Flavonifractor within the family Ruminococcaceae and had highest similarity to Pseudoflavonifractor capillosus ATCC 29799 T (96.7 % sequence similarity), followed by Flavonifractor plautii ATCC 29863 T (96.4 %). Acetate and butyrate were produced by strain 3BBH22 T as metabolic end-products. The major cellular fatty acids were C14 : 0, C16 : 0, C18 : 1ω9c, C16 : 0 dimethyl acetal, C18 : 0 and C18 : 2ω6,9c. No respiratory quinones were detected. In contrast to F. plautii JCM 32125 T , strain 3BBH22 T did not degrade quercetin, one of the flavonoids. P. capillosus JCM 32126 T also did not. Strain 3BBH22 T was differentiated from P. capillosus JCM 32126 T by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22 T represents a novel species in a novel genus of the family Ruminococcaceae, for which the name Lawsonibacter asaccharolyticus gen. nov., sp. nov. is proposed. The type strain of L. asaccharolyticus is 3BBH22 T (=JCM 32166 T =DSM 106493 T ).

Neptunomonas phycophila sp. nov. isolated from a culture of Symbiodinium sp., a dinoflagellate symbiont of the sea anemone Aiptasia tagetes.

PubMed

Frommlet, Jörg; Guimarães, Bárbara; Sousa, Lígia; Serôdio, João; Alves, Artur

2015-03-01

A Gram-stain-negative, facultatively anaerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain SYM1(T), was isolated from a culture of Symbiodinium sp., an algal symbiont of the sea anemone Aiptasia tagetes collected in Puerto Rico. Growth was observed at 4-40 °C (optimum 30 °C), at pH 5.0-11.0 (optimum pH 8.0) and with 0.5-8 % (optimum 2 %) (w/v) NaCl. Phylogenetic analyses of 16S rRNA gene sequences showed that strain SYM1(T) was a member of the genus Neptunomonas with the type strain of Neptunomonas naphthovorans as the closest phylogenetic relative with a pairwise sequence similarity of 98.15 %. However, DNA-DNA relatedness between strain SYM1(T) and N. naphthovorans CIP 106451(T) was 24 %. Moreover, strain SYM1(T) could be distinguished from its closest relative by several phenotypic characteristics such as NaCl, pH and temperature tolerance, nitrate reduction and utilization of carbon substrates. The major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content of strain SYM1(T) was 45 mol%. Ubiquinone-8 (Q-8) was the only respiratory quinone detected. Based on a polyphasic taxonomic characterization, strain SYM1(T) represents a novel species of the genus Neptunomonas, for which the name Neptunomonas phycophila sp. nov. is proposed. The type strain is SYM1(T) ( = LMG 28329(T) = CECT 8716(T)). © 2015 IUMS.

Aquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond.

PubMed

Han, Ji-Ru; Fang, Dong-Bo; Xia, Hai-Feng; Chen, Guan-Jun; Du, Zong-Jun

2017-06-01

A Gram-stain-negative, non-motile, rod-shaped, red-pigmented, facultatively anaerobic bacterium, designated SS2-9T, was isolated from sediment collected from a sea cucumber culture pond located in Rongcheng, Shandong province, China. Cells of strain SS2-9T were approximately 0.3-0.5 µm in width and 1.5-6.0 µm in length. The strain was able to grow at 10-37 °C, at pH 6.5-8.5 and in the presence of 0.5-6.0 % (w/v) NaCl. It grew optimally at 28 °C and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content was 34.5 mol% and the sole respiratory quinone was menaquinone 6 (MK-6). The predominant cellular fatty acids were C15 : 0, iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SS2-9T was phylogenetically related to members of the genus Aquimarina and was closely related to Aquimarina amphilecti 92VT (97.29 % similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SS2-9T was considered to represent a novel species of the genus Aquimarina, for which the name Aquimarina rubra sp. nov. is proposed. The type strain is SS2-9T (=KCTC 52274T=MCCC 1H00142T).