Bacterial diversity in the cave of Altamira.

5 pages, 1 figure, 2 tables, 14 references. Electronic Newsletter. CSIC Thematic Network on Cultural Heritage and Network on Science and Technology for the Conservation of Cultural Heritage Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Apartado de Correos 1052, 41080 Sevilla (Spain).The study of microorganisms involved in deterioration of prehistoric paintings is of great importance to preserve these singular samples of cultural heritage. This study presents, as an example, results from a research carried out in Altamira Cave (Cantabria, Spain). Altamira Cave contains numerous and well known paintings from the Upper Palaeolithic, dated back around 15,000 years. This work focused in understanding the microorganisms inhabiting this singular system and the potential consequences of its microbial diversity for conservation of these valuable paintings.The authors acknowledge financial support from the Spanish Ministry of Education and Science (project CGL2006-07424/BOS) and the Spanish Ministry of Culture.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

Procedimiento de estabilización de biomoléculas

La presente invención se refiere a un procedimiento para la estabilización de biomoléculas caracterizado porque dicha estabilización se consigue manteniendo la viscosidad del medio en el cual se encuentran dichas biomoléculas. Es de aplicación a un amplio número de biomoléculas tales como ATP o NADH y permite la utilización de las mismas en procedimientos analíticos, clínicos o médicos que se vayan a llevar a cabo en condiciones no adecuadas para el mantenimiento de su estabilidad.Peer reviewedConsejo Superior de Investigaciones CientíficasB1 Patente sin examen previ

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

A procedure to evaluate the resistance to biological colonization as a characteristic for product quality of ceramic roofing tiles

9 pages, 5 figures, 4 tables, 22 references. The authors acknowledge the collaboration of the company Cerámica La Escandella (Spain) in supplying the samples of ceramic roofing tiles, and the advice and support by Dr. José Enrique Frias (Servicio de Cultivos Biológicos, Instituto de Biologia Vegetal y Fotosíntesis, CSIC, Seville, Spain) who provided us with the cyanobacterial strains used in this work.Ceramic roofing tiles suffer deterioration through time due to environmental exposure. Biological colonization affects the appearance and integrity of building materials, such as roofing tiles. The resistance to biocolonization represents an important property affecting the product quality of ceramic roofing tiles. While natural colonization of roofing tiles by organisms is a progressive, heterogeneous, and slow process, laboratory assessment of this phenomenon requires a sensitive procedure that can be carried out within a reasonable period of time. Different microorganisms have been evaluated and the use of phototrophs, specifically the cyanobacterium Oscillatoria, presented several advantages such as good adherence, homogeneous growth on surfaces, and the chlorophyll-autofluorescence which can be used for a sensitive detection. Colonization by Oscillatoria on roofing tiles was assessed by measuring the autofluorescence of cells. This study proposes the use of specific cyanobacterial cells and a simple method for monitoring biofilm formation and biological colonization of roofing tiles.. This study was funded by project PET2007-0080 from the Spanish Ministry of Science and Innovation.Peer 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

Reduction of net sulfide production rate by nitrate in wastewater bioreactors. Kinetics and changes in the microbial community

15 páginas, 7 figuras, 5 tablas, 44 referencias.-- [email protected] addition stimulated sulfide oxidation by increasing the activity of nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), decreasing the concentration of dissolved H2S in the water phase and, consequently, its release to the atmosphere of a pilot-scale anaerobic bioreactor. The effect of four different concentrations of nitrate (0.12, 0.24, 0.50, and 1.00 mM) was investigated for a period of 3 days in relation to sulfide concentration in two bioreactors set up at Guadalete wastewater treatment plant (Jerez de la Frontera, Spain). Physicochemical variables were measured in water and air, and the activity of bacteria implicated in the sulfur and nitrogen cycles was analyzed in the biofilms and in the water phase of the bioreactors. Biofilms were a net source of sulfide for the water and gas phases (7.22±5.3 μmol s−1) in the absence of nitrate dosing. Addition of nitrate resulted in a quick (within 3 h) decrease of sulfide both in the water and atmospheric phases. Sulfide elimination efficiency in the water phase increased with nitrate concentrations following the Michaelis–Menten kinetics (Ks=0.63 mM NO3 −). The end of nitrate addition resulted in a recovery or increase of initial net sulfide production in about 3 h. Addition of nitrate increased the activity of NR-SOB and decreased the activity of sulfate-reducing bacteria. Results confirmed the role of NR-SOB on hydrogen sulfide consumption coupled with nitrate reduction and sulfate recycling, revealing Sulfurimonas denitrificans and Paracoccus denitrificans as NR-SOB of great importance in this process.We acknowledge the support of the grants P06-RNM-01787, P11-RNM-7199, the PAI groups RNM-214 and BIO-288 from Consejería de Innovación, Ciencia y Empresa, Junta de Andalucía, Spain and CTM2009-10736 from the Ministerio de Innovación y Ciencia, Spain, which include cofinancing from FEDER funds. S. Papaspyrou was funded by a JAE-Doc fellowship (Programa JAE, JAE-Doc109, Spanish National Research Council) and a Marie Curie ERG action (NITRICOS, 235005, European Union).Peer reviewe

La interacción de procesos hidrológicos, químicos y microbiológicos en la formación de películas flotantes ricas en hierro en ambientes acuáticos de pH circumneutro

17 páginas.-- 3 figuras.-- 4 tablas.-- 53 referencias.-- Postprint (Versión editorial)[EN]: The direct contribution of microbial activity to the formation of iron-oxide minerals is difficult to prove in wetlands due to the high reactivity of solid iron phases with different compounds and the variety of redox processes that may occur at each oxic-anoxic boundary. Here, we propose an explanation for the formation of iron-oxide films in wetlands and groundwater seepage areas fed by sandy aquifers based on the interaction of hydrological, chemical and microbiological processes under circumneutral conditions. The presence of a floating iron-oxide film was found to create a boundary at the air-water interface that maintains a suboxic and slightly acidic environment below the film compared with the environments obtained in other free-film wetland areas. The water trapped below this film had an average pH of 6.1, was particularly poor in O2, HCO–3, Na+, Ca2+, Mg2+, K+, and Tot-S, and has high concentrations of Tot-P, Tot-Fe, NH+4 and Zn. The formation of a floating iron-oxide film was reproduced under anaerobic conditions after progressive enrichment through the incubation of natural sediment samples in the laboratory. Heterotrophic bacteria belonging to the genus Enterobacter were the dominant bacteria in the enrichments that resulted in the formation of a floating iron-oxide film. The X-ray diffraction patterns showed that the presence of two-line ferrihydrite was common to the iron-oxide films collected in both the natural environment and the laboratory cultures, whereas other iron-oxides (goethite and low-crystalline lepidocrocite) were observed only in the natural environment. This study highlights the role of ubiquitous bacteria, which are generally considered unimportant participants in iron-transformation processes in the environment, and the contribution of both biological and non-biological processes to iron oxidation in natural systems under circumneutral conditions.[ES]: En los humedales, es difícil probar que la actividad microbiana sea la responsable de la formación de óxido de hierro mineral debido, tanto a la gran reactividad del hierro en fase sólida con diferentes sustancias, como a la variedad de procesos redox que pueden ocurrir en cada interfase óxica-anóxica. El presente trabajo propone una explicación, basada en la interacción de procesos hidrológicos, químicos y microbiológicos en condiciones circumneutras, para explicar la formación de un film de óxido de hierro en humedales y manaderos donde aflora agua subterránea proveniente de acuíferos de arenas silíceas. Además, la presencia de un film de óxido de hierro que flota sobre la interfase agua-aire genera condiciones subóxicas y ligeramente ácidas en el agua que queda atrapada debajo, y que son muy distintas a otras zonas libres de film en el mismo humedal. Este agua atrapada bajo el film se caracterizó por presentar un pH medio de 6.1, una menor concentración de O2, HCO–3, Na+, Ca2+, Mg2+, K+, y S total, pero una mayor riqueza en P total, Fe total, NH+4 y Zn. La formación de un film flotante de óxido de hierro se reprodujo en el laboratorio, en condiciones anaeróbicas, tras el enriquecimiento progresivo de las muestras del sedimento natural que habían sido incubadas. En dichos enriquecimientos, donde se produjeron films flotantes de óxido de hierro, la bacteria dominante perteneció al género Enterobacter. Mediante difracción por rayos X, se encontró ferrihidrita con estructura en doble cadena, tanto en el film de muestras naturales como de cultivos de laboratorio. Además se encontraron otros tipos de óxidos minerales (goetita y lepidocrocita de pobre cristalización) sólo en las muestras naturales de film. El presente estudio muestra la relevancia de bacterias ubicuas, hasta ahora consideradas sin importancia en procesos naturales de transformación del hierro, y la participación tanto de procesos bióticos como abióticos en la oxidación del hierro en sistemas naturales sometidos a condiciones circumneutras.We are grateful to Han Golterman for his support and suggestions. We thank Lotte Fleskens and Christien van der Zwart for collaborating with the sediment collection and P-fractionation at the laboratory. This study was partially supported by the Spanish Ministry of Education and Science (CGL2004-03927-C02-01/BOS)Peer reviewe

Investigación sobre la producción vitivinícola en el bajo valle del Ebro (ss. VII-I a. C.): un proyecto interdisciplinar de arqueología experimental

We present the results of an interdisciplinary project aimed at the experimental reproduction of wine making processes (production, storage, and conservation) according to historical-archaeological data from Iron Age (7th-1st centuries BC) north-eastern Iberia. The experiment has documented an annual cycle, from grape harvesting, production of must, its transformation into wine and the subsequent conservation of the resulting drink. In order to check its progress, its quality and suitability for consumption, the alcoholic degree, total acidity, pH, volatile acidity, colour, and potassium concentration were analysed and evaluated. In addition, quarterly wine tastings were conducted to assess its organoleptic quality and degree of taste acceptability. A basic microbiological control of the main yeasts and bacteria identified during the process was carried out, too. The results provide fundamental data on the stages of wine production process and preservation conditions, both of which are key to analysing the role of wine consumption in the social practices of Iron Age communities in the north-east of the Iberian Peninsula.Se presentan los resultados de un proyecto interdisciplinar que ha tenido como objetivo la reproducción experimental de los procesos de producción, almacenamiento y conservación del vino de acuerdo a los datos histórico-arqueológicos procedentes del nordeste peninsular durante la Edad del Hierro (ss. VII-I a. C.). El experimento ha documentado el ciclo anual, desde la recolección de la uva, la elaboración del mosto y su transformación en vino, hasta la posterior conservación de la bebida resultante. Con el fin de comprobar su evolución, calidad y aptitud para el consumo, se han analizado y valorado el grado alcohólico, la acidez total, el pH, la acidez volátil, el color y la concentración de potasio. Asimismo se han realizado catas trimestrales para determinar la calidad organoléptica y su grado de aceptabilidad gustativa. Paralelamente, se ha efectuado un control microbiológico básico de las principales levaduras y bacterias localizadas durante el proceso. Los resultados aportan datos relevantes sobre las fases del proceso productivo y las condiciones de conservación del vino, ambas claves para analizar el papel de su consumo en la práctica social de las comunidades de la Edad del Hierro del noreste peninsular

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe