165 research outputs found
KarsTS: an R package for microclimate time series analysis
No full textKarsTS 2.2 is free, open-source, R-based software for microclimate time series, especially suited to the study of underground or highly insulated environments. The time series of interest include air temperature, humidity, and CO2 and 222Rn content, amongst others. These time series usually pose problems such as gaps, outliers, noise or relative shortness. KarsTS was born as a package for gap filling and thus, it offers multiple univariate and multivariate gap-filling tools well suited to these variables. However, as KarsTS was intended to be a self-sufficient program, it soon grew to encompass several tools for linear and nonlinear time series analysis, preprocessing and plotting. Indeed, many of these variables show a nonlinear behavior that is often disregarded; for this reason, we aim to spread and facilitate the use of some methodologically appropriate analysis tools, even amongst researcher that do not feel comfortable using a console. In this paper, we introduce an overview of KarsTS functionality and we show its potential through some practical application examples on four-year time series of temperature from the Rull cave (Spain).This research was funded by the Spanish Ministry of Economy and Competitiveness Projects [CGL2011-25162, CGL2016-78318-C2-1-R, CGL2016-78318-C2-2-R and RTI2018-099052-B-I00]. A post-doctoral research fellowship was awarded to S. Cuezva by the University of Almería (Hipatia Programme)
The biogeochemical role of Actinobacteria in Altamira Cave, Spain
No full text10 pages, 8 figures, 2 tables, 34 references. Cuezva, Soledad et al.--The walls and ceiling of Altamira Cave, northern Spain, are coated with different coloured spots (yellow, white and grey). Electron microscopy revealed that the grey spots are composed of bacteria and bioinduced CaCO 3 crystals. The morphology of the spots revealed a dense network of microorganisms organized in well-defined radial and dendritic divergent branches from the central area towards the exterior of the spot, which is coated with overlying spheroidal elements of CaCO 3 and CaCO 3 nest-like aggregates. Molecular analysis indicated that the grey spots were mainly formed by an unrecognized species of the genus Actinobacteria. CO 2 efflux measurements in rocks heavily covered by grey spots confirmed that bacteria-forming spots promoted uptake of the gas, which is abundant in the cave. The bacteria can use the captured CO 2 to dissolve the rock and subsequently generate crystals of CaCO 3 in periods of lower humidity and/or CO 2. A tentative model for the formation of these grey spots, supported by scanning electron microscopy and transmission electron microscopy data, is proposed. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.This research was supported by the Spanish Ministry of Science and Innovation, project CGL2010-17108 BTE and Consolider programme, project CSD2007-00058. S.C. was funded by a postdoctoral fellowship from the Spanish Ministry of Science and Innovation, research programme Juan de la Cierva. E.P. was supported by a CSIC JAEPredoctoral grant. L.P. was supported by Slovenian Research Agency, research programme P1-0198. Altamira Cave Research Centre and Museum staff are thanked for their collaboration throughout the research period.Peer reviewedPeer Reviewe
Role of microorganisms in processes of capture and emission of greenhouse gases in underground environments
No full textTesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Biológicas, leída el 17/02/2023. Tesis formato europeo (compendio de artículos)Los ambientes kársticos son los ecosistemas subterráneos más representativos a escala global ya que ocupan aproximadamente el 20 % de la superficie terrestre, albergan cavidades próximas a la superficie y forman parte de lo que se conoce como Zona Crítica de la Tierra. A pesar de que podrían jugar un papel importante en la regulación de la composición de la atmósfera externa, los ecosistemas subterráneos aún no han sido incluidos en las estimaciones globales de los balances de los principales GEI, pero son cada vez más numerosos los trabajos de investigación en este campo...Karstic environments are the most representative underground ecosystems on a global scale since they cover approximately 20% of the land surface of the Earth and contain shallow caves that belong to the Critical Zone of the Earth. Although they could play an important role in regulation of the external atmosphere composition, the underground ecosystems have not yet been included in the annual carbon balances of the main GHGs. However, the research interest in this field has recently increased...Fac. de Ciencias BiológicasTRUEunpu
Rare Earth Elements in a Speleothem Analyzed by ICP-MS, EDS, and Spectra Cathodoluminescence.
No full textSpectra cathodoluminescence (CL) emissions of a stalactite from Castañar cave (west-central Spain) exhibit spatially resolved spectra patterns of Mn2þ and rare earth elements (REE3þ). Although the REE3þ signal is smoothed in the speleothem background sample, the REE-enrichment in some growth layer derives from the presence of cerite, xenotime, monazite, and cerianite in the shale matrix. The spectra CL of both host rock and some calcite-aragonite layers show a wide range of spectral luminescence emissions attributed to REE3þ, mainly Sm3þ, Dy3þ, and Ce3þ. The high Mn2þ-REE3þ anomalies in the inner calcite-aragonite layer could indicate its growth during a phase with stronger weathering of host rock and a more active dynamic hydrology.This research was supported by the Spanish Ministry of Science (project CGL2010-17108=BTE) and in agreement with the Scientific Cooperation between the Museo Nacional de Ciencias Naturales (CSIC) and the Department of Industry, Energy and Environment of the Extremadura Autonomous Region (FEOGA ORIENTACION-FEDER funds). A. Fernandez-Cortes benefits from the JAE-Doc Program (CSIC) and S. Cuezva from a Juan de la Cierva fellowship (MICIIN).Peer Reviewe
Preliminary study about microestructure of the fossil bones from Somosaguas mammals (Middle Miocene, Madrid, Spain)
No full text[ES] La histología de los huesos fósiles de los mamíferos del yacimiento paleontológico
mioceno de Somosaguas se encuentra muy bien preservada. En este trabajo
se describen microestructuras de tejido óseo laminar (osteonas, laminillas circunferenciales
y láminas intersticiales) y no laminar hasta el nivel celular. Las
microestructuras óseas pueden encontrarse afectadas por dos tipos de alteraciones,
una de ellas generadas por organismos saprófitos durante la etapa bioestratinómica
y la otra de origen y temporalidad desconocidos. Todo ello nos proporciona
mucha información sobre la paleobiología y tafonomía de los fósiles de mamíferos
de Somosaguas.[EN] Paleohistology of fossil mammal bones belonging to Somosaguas site is very
well preserved. In this work we describe bone microestructures such us laminar
bone (osteones, lamelae) and non laminar bone, till the celular level. Two kinds
of alterations may affect the bone, one of them generated by saprophyt organisms
during biostratinomic stages, an the other of unknown origin. This give us a source of new information about paleobiology and taphonomy of fossil mammals.Peer reviewe
Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls
No full textCastañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.This research was supported by the Spanish Ministry of Science and Innovation through project PID2019-110603RB-I00 and the collaboration of projects RTI2018-099052-B-I00 and PID2020-114978GB-I00, MCIN/AEI/FEDER/UE/10.13039/501100011033. This is a contribution from CSIC Interdisciplinary Thematic Platform Open Heritage: Research and Society (PTI-PAIS)
Radiolysis via radioactivity is not responsible for rapid methane oxidation in subterranean air
No full textAtmospheric methane is rapidly lost when it enters humid subterranean critical and vadose zones (e.g., air in soils and caves). Because methane is a source of carbon and energy, it can be consumed by methanotrophic methane-oxidizing bacteria. As an additional subterranean sink, it has been hypothesized that methane is oxidized by natural radioactivity induced radiolysis that produces energetic ions and radicals, which then trigger abiotic oxidation and consumption of methane within a few hours. Using controlled laboratory experiments, we tested whether radiolysis could rapidly oxidize methane in sealed air with different relative humidities while being exposed to elevated levels of radiation (more than 535 kBq m-3) from radon isotopes 222Rn and 220Rn (i.e., thoron). We found no evidence that radiolysis contributed to methane oxidation. In contrast, we observed the rapid loss of methane when moist soil was added to the same apparatus in the absence of elevated radon abundance. Together, our findings are consistent with the view that methane oxidizing bacteria are responsible for the widespread observations of methane depletion in subterranean environments. Further studies are needed on the ability of microbes to consume trace amounts of methane in poorly ventilated caves, even though the trophic and energetic benefits become marginal at very low partial pressures of methane
Dominance of Arcobacter in the white filaments from the thermal sulfidic spring of Fetida Cave (Apulia, southern Italy)
No full textThe thermal spring of Fetida Cave, a still active sulfuric acid cave opening at sea level and located in Santa Cesarea Terme, southeastern Salento (Apulia region, Southern Italy) hosts abundant floating white filaments. The white filaments were mainly composed of sulfur crystals surrounded by microbial mass of the phyla Epsilonbacteraeota, Proteobacteria, Bacteroidetes, and Patescibacteria. The most abundant genus in the white filaments collected from the waters in the innermost part of the cave dominated by sulfidic exhalations was Arcobacter. This abundance can be related to the higher concentration of sulfide dissolved in water, and low oxygen and pH values. Conversely, lower Arcobacter abundances were obtained in the filaments collected in the entrance and middle part of the cave, where sulfidic water mixes with seawater, as the cave is subjected to tides and the mixing of fresh (continental) with marine water. The geochemical analysis of water and atmospheric gases confirmed these environmental constraints. In fact, the highest concentrations of H2S in the air and water were recorded closest to the spring upwelling in the innermost part of the cave, and the lowest ones near the cave entrance. The metabolic versatility of Arcobacter might provide a competitive advantage in the colonization of water bodies characterized by high sulfide, low oxygen, and dynamic fluid movement
EnvironmentalWaveletTool: Continuous and discrete wavelet analysis and filtering for environmental time series
No full textA MATLAB-based computer code has been developed for the simultaneous wavelet analysis and filtering of several environmental time series, particularly focused on the analyses of cave monitoring data. The continuous wavelet transform, the discrete wavelet transform and the discrete wavelet packet transform have been implemented to provide a fast and precise time–period examination of the time series at different period bands. Moreover, statistic methods to examine the relation between two signals have been included. Finally, the entropy of curves and splines based methods have also been developed for segmenting and modeling the analyzed time series. All these methods together provide a user-friendly and fast program for the environmental signal analysis, with useful, practical and understandable results.This research was supported by the Spanish Ministry of Science and Innovation, projects CGL2011-25162 and CGL2010-17108. A pre-doctoral research fellowship was awarded to C. Pla for the CGL2011-25162 research project. S. Cuezva was funded by a postdoctoral fellowship from the Spanish Ministry of Science and Innovation, research program Juan de la Cierva
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