Identification and characterization of a freshwater Pyrococcus sp. strain PK 5017 and identification of pfu-like IS elements in Thermococcus sibiricus MM 739

12 pages, 7 figures, 1 table, 32 references.A strictly anaerobic, hyperthermophilic Pyrococcus sp. strain PK 5017 (PK 5017) was isolated from a freshwater hot spring in Thailand. Cells of strain PK 5017 are irregular cocci occurring singly and in pairs with a diameter range of 0.7-1.2 µm. Temperature, pH and NaCl concentration ranges for growth are 75-105 oC (opt. temp. = 95-100 oC), pH 5-7.8 (opt. pH = 7.2) and 2.5-IS-pfu-Ts1> and >IS-pfu-Ts2> are identified in the complete genome sequence of Thermococcus sibiricus MM 739. Pyrococcus sp. strain PK 5017 = Pyrococcus sp. strain Pikanate 5017 = JCM17043 = ATCC BAA-2246.This work was supported by the Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (RGI 2553-06) and Silpakorn University Research and Development Institute (SURDI 54/01/18 and SURDI 55/01/05). JMG and MCP acknowledge support from a CSIC movility program, PA1001993 and PA1002058, and the Andalusian Government Bio288 which included FEDER funds.Peer Reviewe

Differentiation of a hyperthermophilic archaeon Pyrococcus sp. Strain Pikanate 5017, by arbitrarily primed PCR

Pyrococcus and Thermococcus are hyperthermophilic archaea in the order Thermococcales. Both genera are strictly anaerobes, gaining energy by fermentation of peptide and several carbohydrates at optimal temperature above 70 ° C. A Pyrococcus sp. strain Pikanate 5017 (PK 5017) was recently isolated from a hot spring in Northern Thailand. The strain PK 5017 is a valuable source of numerous genes encoding thermostable enzymes. Growth kinetics determined at various temperatures (75-105 ° C) indicates that strain PK5017 is a fast growing archaeon. An arbitrarily primed PCR (AP-PCR) technique was successfully applied to differentiate the genome sequences of six members of Thermococcales. Two single primers, ARB-1f (5’ ATGAG GACT GAAA CCATT 3’) and ARB-2f (5’ GTAAA ACGA CGGC CAGT 3’), are effective in producing polymorphisms of the PCR products at 3-10 ng of DNAs. The unique AP-PCR fingerprints distinguish the strain PK5017 from P. furiosus, P. horikoshii, P. abyssi, T. litoralis, and T. celer. The results indicate a clear distinction of genome sequences among Pyrococcus and Thermococcus genera.This work was supported by a grant from the Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (Grant number RGI 2553-06). JMG and MCP acknowledge the support from a CSIC movility program, PA1001993 and PA1002058, and the Andalusian Government Bio288Peer Reviewe

Fervidobacterium thailandense sp. nov., an extremely thermophilic bacterium isolated from a hot spring

4 páginas.-- 2 figuras.-- 19 referencias.-- Two supplementary tables and four supplementary figures are available with the online Supplementary Material.Strain FC2004T, a strictly anaerobic, extremely thermophilic heterotroph, was isolated from a hot spring in Thailand. Typical cells of strain FC2004T were rod shaped (0.5–0.6×1.1–2.5 µm) with an outer membrane swelling out over an end. Filaments (10–30 µm long) and membrane-bound spheroids containing two or more cells inside (3–8 µm in diameter) were observed. The temperature range for growth was 60–88°C (optimum 78–80°C), pH range was 6.5–8.5 (optimum pH 7.5) and NaCl concentration range was 0 to <5 g l−1 (optimum 0.5 g l−1). S0 stimulated growth yield. S2O3 2– and NO3 − did not influence growth. Glucose, maltose, sucrose, fructose, cellobiose, CM-cellulose and starch were utilized for growth. The membrane was composed mainly of the saturated fatty acids C16:0 and C18:0. The DNA G+C content was 45.8 mol%. The 16S rRNA gene sequence of strain FC2004T revealed highest similarity to species of the genus Fervidobacterium : F. pennivorans DSM 9078T (97–96 %), F. islandicum AW-1 (96 %), F. changbaicum CBS-1T (96 %), F. islandicum H21T (95 %), F. nodosum Rt17-B1T (95 %), F. riparium 1445tT (95 %) and F. gondwanense AB39T (93 %). Phylogenetic analysis of 16S rRNA gene sequences and average nucleotide identity analysis suggested that strain FC2004T represented a novel species within the genus Fervidobacterium , for which the name Fervidobacterium thailandense sp. nov. is proposed. The type strain is FC2004T (=JCM 18757T=ATCC BAA-2483T).Peer reviewe

Paving the way for research findings: writers' rhetorical choices in education and applied linguistics

Notwithstanding the existence of previous investigations into how research results are presented in different academic disciplines, fewer studies have looked into how authors pave the way for their results, the interdisciplinary differences in ‘result pavements’, and the interconnections between their communicative functions and linguistic choices. Using the techniques of genre analysis, I have analyzed two corpora of research reports in applied linguistics and education in order to identify the possible ways in which experienced writers schematically pave the way for their findings. Using evidence based on authentic research articles, this study demonstrates how writers set the stage for their research results by (i) demonstrating their control of the structure and flow of result-related information, (ii) connecting past research with a current finding while furnishing pertinent background elements that lead the readership progressively to specific findings, (iii) regenerating readers’ interest in their initial research purposes, and (iv) deploying locatives to embed results in a ‘space-saving strategy’ aimed at presenting an abridged Results section. I have also analyzed interdisciplinary differences in the frequencies of these rhetorical steps and the range of intricate linguistic mechanisms employed by authors as communicative resources in each step to establish a smooth rhetorical transition that sets the stage for their research results

Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species

21 páginas.-- 12 figuras.-- 5 tablas.--31 referenciasHorizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermotogae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target of analysis. Transposases are key proteins involved in genomic DNA rearrangements. A comprehensive comparative analysis, including phylogeny, non-metric multidimensional scaling analysis of tetranucleotide frequencies, repetitive flanking sequences and divergence estimates, was performed on the transposase genes detected in four Fervidobacterium genomes: F. nodosum, F. pennivorans, F. islandicum and a new isolate (Fervidobacterium sp. FC2004). Transposase sequences were classified in different groups by their degree of similarity. The different methods used in this study pointed that over half of the transposase genes represented putative HGT events with closest relative sequences within the phylum Firmicutes, being Caldicellulosiruptor the genus showing highest gene sequence proximity. These results confirmed a direct evolutionary relationship through HGT between specific Fervidobacterium species and thermophilic Firmicutes leading to potential gene sequence and functionality sharing to thrive under similar environmental conditions. Transposase-encoding genes represent suitable targets to approach the plasticity and potential mosaicism of bacterial genomes.This study was supported by funding through projects from the Spanish Ministry of Economy and Competitiveness (CSD2009-00006 and CGL2014-58762-P) and the Regional Government of Andalusia (RNM2529 and BIO288). The participation of FEDER funds is acknowledgedPeer Reviewe

A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei

Pyrococcus species are hyperthermophilic members of the order Thermococcales, with optimal growth temperatures approaching 100°C. All species grow heterotrophically and produce H2 or, in the presence of elemental sulfur (S°), H2S. Pyrococcus woesei and P. furiosus were isolated from marine sediments at the same Vulcano Island beach site and share many morphological and physiological characteristics. We report here that the rDNA operons of these strains have identical sequences, including their intergenic spacer regions and part of the 23S rRNA. Both species grow rapidly and produce H2 in the presence of 0.1% maltose and 10-100 μM sodium tungstate in S°-free medium. However, P. woesei shows more extensive autolysis than P. furiosus in the stationary phase. Pyrococcus furiosus and P. woesei share three closely related families of insertion sequences (ISs). A Southern blot performed with IS probes showed extensive colinearity between the genomes of P. woesei and P. furiosus. Cloning and sequencing of ISs that were in different contexts in P. woesei and P. furiosus revealed that the napA gene in P. woesei is disrupted by a type III IS element, whereas in P. furiosus, this gene is intact. A type I IS element, closely linked to the napA gene, was observed in the same context in both P. furiosus and P. woesei genomes. Our results suggest that the IS elements are implicated in genomic rearrangements and reshuffling in these closely related strains. We propose to rename P. woesei a subspecies of P. furiosus based on their identical rDNA operon sequences, many common IS elements that are shared genomic markers, and the observation that all P. woesei nucleotide sequences deposited in GenBank to date are >99% identical to P. furiosus sequences.This work was supported by a grant from the Knut and Alice Wallenberg Foundation, and by Grant MCB 9809352 to F.T.R. from the National Science Foundation. J.M.G. also acknowledges support from the Spanish Ministry of Science and Technology through the Ramon y Cajal Programme and Grant REN2002-00041/GLO. This is Contribution No. 04-620 from the Center of Marine Biotechnology.Peer Reviewe

Evidencia de transferencia horizontal de genes mediante el estudio de las transposasas en el género Fervidobacterium

Comunicación oral presentada en la XII Reunión Red Nacional Organismos Extremófilos. (REDEX2014) 031 Sesión 4 : Metagenómica y Fisiología, pag. 42. Libro de resumenes.Los fenómenos de transferencia horizontal de genes (HGT) juegan un papel relevante en la fisiología y la evolución de los microorganismos, especialmente en procariotas termófilos. Los genomas de algunos miembros del phylum Thermotogae (por ejemplo, Thermotoga spp.) se proponen como un mosaico formado por genes con diversos orígenes. Las transposasas son proteínas claves que intervienen en reordenamientos de ADN genómico dentro de un genoma, así como en transferencias de material genético entre organismos, incluyendo diferentes especies de categorías taxonómicas alejadas. Este estudio presenta un nuevo enfoque para detectar procesos de HGT mediante el estudio de los genes que codifican para transposasas en genomas del género Fervidobacterium. Para ello, se han llevado a cabo análisis filogenéticos, multivariables de frecuencia de uso de codones y de frecuencia de tetranucleótidos, así como la determinación y comparación de las secuencias repetitivas invertidas asociadas a las transposasas de tres especies: F. nodosum, F. pennivorans y una nueva cepa, Fervidobacterium sp. FC2004, recientemente aislada en nuestro laboratorio. Las transposasas detectadas se clasificaron en diferentes grupos atendiendo a su grado de similitud. Los análisis filogenéticos, multivariables y la comparación entre secuencias repetitivas invertidas coincidían en distinguir varios grupos de transposasas como indicadores de posibles fenómenos de HGT. Estos casos de HGT se muestran estrechamente relacionados con transposasas de diferentes representantes del phylum Firmicutes, siendo Caldicellulosiruptor uno de los géneros con representantes más cercanos en varios de los grupos estudiados. Los resultados obtenidos sugieren la existencia de varios fenómenos de HGT entre Fervidobacterium spp. y Firmicutes termófilos que se supone que ha llevado a estos grupos a facilitar su adaptación a las distintas condiciones existentes en sus ambientes extremos que frecuentemente cohabitan.Financiación: MICROGEN (Consolider CSD2009-00006; Ministerio de Economía y Competitividad) y BIO288 (Junta de Andalucía), ambos cofinanciados con fondos FEDER.Peer Reviewe

Evidence of directed horizontal gene transfer by transposase gene analyses in Fervidobacterium species.

Poster presentación en el 10th International Congress on Extremophiles (Extremophiles 2014), September 7-11, 2014, Saint Petersburg, RussiaHorizontal Gene Transfer events play an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the phylum Thermotogae (e. g., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target genes of analysis. Transposases are key proteins involved in genomic DNA rearrangements within a genome and transferences between organisms, including different species from distantly related taxonomic categories. A comprehensive genome comparative analysis, including phylogeny, codon usage, and %GC content, is being performed for the transposases and related sequences present in three Fervidobacterium species: F. nodosum, F. pennivorans and including a newly reported isolate (candidate F. thailandensis). These transposases could be classified in different groups attending to their level of similarity. Only a low fraction of these sequences showed high similarity to transposase sequences represented in members of the phylum Thermotogae. Interestingly, sequence phylogeny, codon usage and %GC content showed that most groups of transposases were closely related to transposase sequences from different representatives of the Firmicutes Phylum. Other taxonomic categories, such as the phylum Nitrospirae and the Domain Archaea, showed relationship to some transposase genes in Fervidobacterium species but at a lower extent. This information suggests a direct evolutive relationship through horizontal gene transfer between specific thermophilic Firmicutes and Fervidobacterium species which leads to sharing genes, genome fragments and potential functionality besides putative environmental habitats.Peer Reviewe

Characterization and identification of two hyperthermophilic bacteria isolated from a hot spring in Thailand: a Thermotoga sp. strain FC 1002 and a Fervidobacterium sp. strain FC 2004

3 figuras, 2 fotografías, 1 tabla, 5 referencias.-- Póster presentado al citado congreso, celebrado del 10-13 de septiembre 2012, en Sevilla, España.-- [email protected] research was financed by the Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (RGI 2553-06) and Silpakorn University Research and Development Institute (SURDI 54/01/18 and SURDI 55/01/05). JMG and MCP acknowledge support from a CSIC movility program, PA1001993 and PA1002058, and the Andalusian Government Bio288 which included FEDER funds.Peer Reviewe

Identification of a putative keratinase gene and analysis of a peptidase S8 Family in a hyperthermophilic, Fervidobacterium sp. Strain FC2004 in Thailand

13 páginas.-- 6 figuras.-- referencias.-- Ponencia presentada en el The 28 Annua! Meeting of the Thai Society for Biotechno!ogy and Intemational Conference, 28th to 30th November, 2016 in Chiang Mai, ThailandA hyperthermophilic Fervidobacterium sp. strain FC2004 was previously isolated from a hot spring in Thailand. A putative gene encoding a proenzyme named in this study ¿ProA1¿ was identified from shotgun sequencing of genomic DNA of the strain FC2004. Predicted 3D-molecule contains a non-homologous signal peptide, a propeptide domain (PD), a catalytic domain (CD) with the typical catalytic triad residues of D169, H207 and S379, and a substrate binding domain (SD). Unlike fervidolysin and islandisin, the ProA1 completely lacks the SD2 domain. Phylogenetic analysis suggests that the ProA1 might be an intermediate isoform between high molecular weight and low molecular weight peptidase S8_subtilases. Although, the strain FC2004 is able to degrade pieces of native feather at high temperature, whether or not the mature ProA1 is active on keratin, the SD plays a role in hydrolyzing keratin substrate and the strain FC2004 might carry a second serine protease with two SDs remains to be investigated.This work was supported by the following grants: The Scientific Promotion and Development Fund, Faculty of Science, Silpakorn University (SFR-SRG-2558-01) and the Silpakorn University Research and Development Institution from Thailand; and the Ministry of Economy and Productivity (Consolider CSD2009-00006) and the Andalusian Government (BIO288) from Spain with participation of FEDER funds.Peer Reviewe