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Speleology in Kazakhstan

Shakalov on 04 Jul, 2018
Hello everyone!   I pleased to invite you to the official site of Central Asian Karstic-Speleological commission ("Kaspeko")   There, we regularly publish reports about our expeditions, articles and reports on speleotopics, lecture course for instructors, photos etc. ...

New publications on hypogene speleogenesis

Klimchouk on 26 Mar, 2012
Dear Colleagues, This is to draw your attention to several recent publications added to KarstBase, relevant to hypogenic karst/speleogenesis: Corrosion of limestone tablets in sulfidic ground-water: measurements and speleogenetic implications Galdenzi,

The deepest terrestrial animal

Klimchouk on 23 Feb, 2012
A recent publication of Spanish researchers describes the biology of Krubera Cave, including the deepest terrestrial animal ever found: Jordana, Rafael; Baquero, Enrique; Reboleira, Sofía and Sendra, Alberto. ...

Caves - landscapes without light

akop on 05 Feb, 2012
Exhibition dedicated to caves is taking place in the Vienna Natural History Museum   The exhibition at the Natural History Museum presents the surprising variety of caves and cave formations such as stalactites and various crystals. ...

Did you know?

That cuesta, hogback is a nonsymetrical ridge due to a gently dipping stratum [16].?

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Featured articles from Cave & Karst Science Journals
Chemistry and Karst, White, William B.
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Karst environment, Culver D.C.
Mushroom Speleothems: Stromatolites That Formed in the Absence of Phototrophs, Bontognali, Tomaso R.R.; D’Angeli Ilenia M.; Tisato, Nicola; Vasconcelos, Crisogono; Bernasconi, Stefano M.; Gonzales, Esteban R. G.; De Waele, Jo
Calculating flux to predict future cave radon concentrations, Rowberry, Matt; Marti, Xavi; Frontera, Carlos; Van De Wiel, Marco; Briestensky, Milos
Microbial mediation of complex subterranean mineral structures, Tirato, Nicola; Torriano, Stefano F.F;, Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Lavagna, Maria Luisa; D’Angeli, Ilenia Maria; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I.; Bontognali, Tomaso Renzo Rezio
Evidence of a plate-wide tectonic pressure pulse provided by extensometric monitoring in the Balkan Mountains (Bulgaria), Briestensky, Milos; Rowberry, Matt; Stemberk, Josef; Stefanov, Petar; Vozar, Jozef; Sebela, Stanka; Petro, Lubomir; Bella, Pavel; Gaal, Ludovit; Ormukov, Cholponbek;
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Your search for electron microscopy (Keyword) returned 29 results for the whole karstbase:
Showing 16 to 29 of 29
The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments, 2007, Barton Hazel A. , Taylor Nicholas M. , Kreate Michael P. , Springer Austin C. , Oehrle Stuart A. And Bertog Janet L.
Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88 reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.

The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments., 2007, Barton Hazel A. , Taylor Nicholas M. , Kreate Michael P. , Springer Austin C. , Oehrle Stuart A, Bertog Janet L.
Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88 reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.

The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments, 2007, Barton H. A. , Taylor N. M. , Kreate M. P. , Springer A. C. , Oehrle S. A. , Bertog J. L.

Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88
reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.


Reticulated filaments in cave pool speleothems: microbe or mineral?, 2008, Melim L. A. , Northup D. E. , Spilde M. N. , Jones B. , Boston P. J. , And Bixby R. J.
We report on a reticulated filament found in modern and fossil cave samples that cannot be correlated to any known microorganism or organism part. These filaments were found in moist environments in five limestone caves (four in New Mexico, U.S.A., one in Tabasco, Mexico), and a basalt lava tube in the Cape Verde Islands. Most of the filaments are fossils revealed by etching into calcitic speleothems but two are on the surface of samples. One hundred eighty individual reticulated filaments were imaged from 16 different samples using scanning electron microscopy. The filaments are up to 75 mm (average 12 mm) long, but all filaments appear broken. These reticulated filaments are elongate, commonly hollow, tubes with an open mesh reminiscent of a fish net or honeycomb. Two different cross-hatched patterns occur; 77% of filaments have hexagonal chambers aligned parallel to the filament and 23% of filaments have diamond-shaped chambers that spiral along the filament. The filaments range from 300 nm to 1000 nm in diameter, but there are two somewhat overlapping populations; one 200400 nm in size and the other 500700 nm. Individual chambers range from 40 to 100 nm with 3040 nm thick walls. Similar morphologies to the cave reticulated filaments do exist in the microbial world, but all can be ruled out due to the absence of silica (diatoms), different size (diatoms, S-layers), or the presence of iron (Leptothrix sp.). Given the wide range of locations that contain reticulated filaments, we speculate that they are a significant cave microorganism albeit with unknown living habits.

Kryogene Karbonate im Hhleneis der Eisriesenwelt, 2008, Sptl, C.
Progressive freezing of calcium- and bicarbonate- bearing cave waters can give rise to high supersaturation and the subsequent precipitation of microscopic calcite crystals and aggregates thereof. These particles are disseminated in the ice of ice caves and may later be concentrated by sublimation or melting of ice to form thin carbonate beds in layered ice (cryogenic carbonates). Such white to light brown, silty to fine sandy layers occur in the rear of the ice-bearing part of the Eisriesenwelt cave (Werfen, Salzburg) and were previously regarded as finely disintegrated limestone powder derived from the cave ceiling. Studies using scanning electron microscopy show that this material consists of 30-200 ?m aggregates of euhedral crystals, which, according to powder Xray diffraction analyses, are near-stoichiometric low-Mg calcite. The crystal aggregates commonly show a conspicuous flat top and resemble larger floating calcite rafts known from calcite-precipitating pools in ice-free caves. There are gradual transitions between these aggregates and skeletal crystal aggregates and (hemi)spherulitic forms, respectively. The small particle size and the skeletal crystal habit strongly argue in favour of rapid crystal growth during freezing of shallow puddles of icy water. This interpretation is corroborated by the highly positive C isotope values, which, in conjunction with the O isotope data, prove the cryogenic origin of these carbonates. The proportion of detrital contamination is very low. This study is the first report of fine-grained cryogenic speleothems in an eastalpine cave. It is supposed that such sediments are more wide spread and thicker layers may represent important paleoenvironmental marker horizons.

Kryogene Calcitpartikel aus der Heilenbecker Hhle in Ennepetal (NE Bergisches Land/Nordrhein-Westfalen), 2008, Richter D. K. , Neuser R. D. , Voigt S.
Calcarenites to -rudites are present between fallen blocks in the Runde Halle of the Heilenbecker Cave in Ennepetal (NE Bergisches Land, Germany) and are mainly composed of four particle types: 1. plait sinter, 2. rhombohedral crystal sinter, 3. spherulites, 4. skeletal crystal sinter. These speleogenic particles were studied using scanning electron microscopy, cathodoluminescence microscopy and mass spectrometry (C/Oisotopes) in order to gain insights into their mode of formation. The very low 18O (6 to 16 VPDB) and 13C values (3 to 7VPDB) strongly suggest that these calcite particles formed in pools on ice during the transition from a glacial to a warm climate period. Growth of these particles apparently occurred during very slow freezing of water. After the ice had melted the cryogenic particles settled between and on the blocks of the cave.

Exploring the secrets of the three-dimensional architecture of phototrophic biofilms in caves, 2009, Roldn M. And Hernndezmarin M.
Caves with dim natural light, and lighted hypogean environments, have been found to host phototrophic microorganisms from various taxonomic groups. These microorganisms group themselves into assemblies known as communities or biofilms, which are associated with rock surfaces. In this work, the phototrophic biofilms that colonise speleothems, walls and floors in three tourist caves (Spain) were studied. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were used to study these organisms and acquire three-dimensional data on their biofilm structure. CLSM was used in a multi-channel mode whereby the different channels map individual biofilm components. Cyanobacteria, green microalgae, diatoms, mosses and lichens were found to be grouped as biofilms that differed according to the sampling sites. The biofilms were classified into six types regarding their environmental conditions. These types were defined by their constituent organisms, the thickness of their photosynthetic layers and their structure. Light-related stress is associated with lower biofilm thickness and species diversity, as is low humidity, and, in the case of artificially illuminated areas, the duration of light exposure

Exploring the secrets of the three-dimensional architecture of phototrophic biofilms in caves, 2009, Roldn M. , Hernndezmarin M.

Caves with dim natural light, and lighted hypogean environments, have been found to host phototrophic microorganisms from various taxonomic groups. These microorganisms group themselves into assemblies known as communities or biofilms, which are associated with rock surfaces. In this work, the phototrophic biofilms that colonise speleothems, walls and floors in three tourist caves (Spain) were studied. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were used to study these organisms and acquire three-dimensional data on their biofilm structure. CLSM was used in a multi-channel mode whereby the different channels map individual biofilm components. Cyanobacteria, green microalgae, diatoms, mosses and lichens were found to be grouped as biofilms that differed according to the sampling sites. The biofilms were classified into six types regarding their environmental conditions. These types were defined by their constituent organisms, the thickness of their photosynthetic layers and their structure. Light-related stress is associated with lower biofilm thickness and species diversity, as is low humidity, and, in the case of artificially illuminated areas, the duration of light exposure.


The mineral assemblage of caves within Salitrari Mountain (Cerna Valley, SW Romania): depositional environment and speleogenetic implications, 2010, Puscas Cristina M. , Onac Bogdan P. , Tamas Tudor

Eighteen minerals belonging to eight chemical groups were identified from three caves within Şălitrari Mountain, in the upper Cerna River basin (Romania) by means of scanning electron microscopy, electron microprobe analysis, and X-ray powder diffraction. One passage in the Great Cave from Şălitrari Mountain, the largest cave investigated, exhibits abnormal relative humidity and temperature ranges, allowing for a particular depositional environment. The cave floor is covered by alluvial sediments (ranging from cobble, sand, and clay to silt-sized material), bear bones, bat guano, and rubble. These materials reacted with percolating meteoric water and hydrogen sulfide-rich hypogene hot solutions, precipitating a variety of secondary minerals. Most of these minerals are common in caves (e.g. calcite, gypsum, brushite), however, some of them (alunite, aluminite, and darapskite) require very particular environments in order to form and persist. Cave passage morphologies suggest a complex speleogenetic history that includes changes from phreatic to vadose conditions. The latter was punctuated by a sulfuric acid dissolution/precipitation phase, partly overprinted by present-day vadose processes. The cave morphology and the secondary minerals associated with the alluvial sediments in these caves are used to unravel the region’s speleogenetic history.


Iron Oxide and Calcite Associated with Leptothrix sp. Biofilms within an Estavelle in the Upper Floridan Aquifer, 2011, Florea Lee J. , Stinson Chasity L. , Brewer Josh, Fowler Rick, Kearns B Joe, Greco Anthony M.

In Thornton’s Cave, an estavelle in west-central Florida, SEM, EDS, and XRD data reveal biofilms that are predominantly comprised of FeOOH-encrusted hollow sheaths that are overgrown and intercalated with calcite. Fragments of this crystalline biofilm adhere to the walls and ceiling as water levels vary within the cave. Those on the wall have a ‘cornflake’ appearance and those affixed to the ceiling hang as fibrous membranes. PCR of DNA in the active biofilm, combined with morphologic data from the tubes in SEM micrographs, point to Leptothrix sp., a common Fe-oxidizing bacteria, as the primary organism in the biofilm. Recent discoveries of ‘rusticles’ in other Florida caves suggest that Fe-oxidizing bacteria may reside elsewhere in Florida groundwater and may play a role in the mobility of trace metals in the Upper Florida aquifer.
SEM micrographs from two marble tablets submerged for five months, one exposed to microbial activity and a second isolated from microbial action, revealed no visible etchings or borings and very limited loss of mass. EDS data from the electron micrographs of the unfiltered tablet document the same FeOOH-encrusted hollow sheaths and similar deposits of calcite as seen in the ‘cornflakes’. These results, combined with water chemistry data imply that the biofilm may focus or even promote calcite precipitation during low-water level conditions when CO2 degasses from the cave pools.


First Steps in Limestone Weathering and Erosion: An Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) approach, 2011, Forns Joan J. , Gmezpujol Llus, Cifre Joan, Hierro Ferran

A combined atomic force microscope (AFM) and scanning electron microscope (SEM) experiment examining the first steps in limestone weathering and erosion is presented. The experiment
deals with the exposure of polished limestone rock tablets to a Western Mediterranean coastal environment and with the rate and patterns of weathering addressed by roughness
quantification and qualitative assessment of nanoforms. Observations show how rock surface roughness increases at high rates after four and six months of exposure, passing from initial roughness RMS values between 14 and 32 mm to values between 396 to 492 mm. From the qualitative SEM approach, it can be concluded that the roughness increase relates with the widening of the space between rock grains and results in the isolation and detaching of rock grains.


Deterioration of the black Drenov Grič limestone on historical monuments (Ljubljana, Slovenia), 2011, Kramar Sabina, Mladenović, Ana, Pristacz Helmut, Mirtič, Breda

The black limestone from Drenov Grič quarry (Central Slove­nia) is considered one of the most beautiful Slovenian natural stones due to its typical color. The limestone was character­ized from mineralogical, chemical, and petrophysical points of view. Furthermore, deterioration phenomena of the limestone from two monuments exposed to indoor and outdoor environ­ments were studied. In situ investigation of two monuments by means of monument mapping has identified several types of deterioration phenomena, such as granular disintegration, flaking, crumbling, efflorescences, crusts, and the presence of microorganisms. Samples were characterized using Opti­cal Microscopy (OM), Scanning Electron Microscopy (SEM) coupled with Energy Dispersive Spectroscopy (EDS), X-Ray Powder Diffraction Analysis (XRD), porosity accessible to wa­ter under vacuum, capillary absorption, Mercury porosimetry (MIP), and Ar-sorption. Although very low values of porosity of the fresh stone as well as slow capillary kinetics were de­termined, both monuments showed severe deterioration as a consequence of the transport and precipitation of soluble salts within the stone.


Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery, 2013, Cheeptham N. , Sadoway T. , Rule D. , Watson K. , Moote P. , Soliman L. C. , Azad N. , Donkor K. K. , Horne D.

Volcanic caves have been little studied for their potential as sources of novel microbial species and bioactive compounds with new scaffolds. We present the first study of volcanic cave microbiology from Canada and suggest that this habitat has great potential for the isolation of novel bioactive substances. Sample locations were plotted on a contour map that was compiled in ArcView 3.2. Over 400 bacterial isolates were obtained from the Helmcken Falls cave in Wells Gray Provincial Park, British Columbia. From our preliminary screen, of 400 isolates tested, 1% showed activity against extended spectrum ß-lactamase E. coli, 1.75% against Escherichia coli, 2.25% against Acinetobacter baumannii, and 26.50% against Klebsiella pneumoniae. In addition, 10.25% showed activity against Micrococcus luteus, 2% against methicillin resistant Staphylococcus aureus, 9.25% against Mycobacterium smegmatis, 6.25% Pseudomonas aeruginosa and 7.5% against Candida albicans. Chemical and physical characteristics of three rock wall samples were studied using scanning electron microscopy and f lame atomic absorption spectrometry. Calcium (Ca), iron (Fe), and aluminum (Al) were the most abundant components while magnesium (Mg), sodium (Na), arsenic (As), lead (Pb), chromium (Cr), and barium (Ba) were second most abundant with cadmium (Cd) and potassium (K) were the least abundant in our samples. Scanning electron microscopy (SEM) showed the presence of microscopic life forms in all three rock wall samples. 16S rRNA gene sequencing of 82 isolates revealed that 65 (79.3%) of the strains belong to the Streptomyces genus and 5 (6.1%) were members of Bacillus, Pseudomonas, Nocardia and Erwinia genera. Interestingly, twelve (14.6%) of the 16S rRNA sequences showed similarity to unidentif ied ribosomal RNA sequences in the library databases, the sequences of these isolates need to be further investigated using the EzTaxon-e database (http://eztaxon-e. ezbiocloud.net/) to determine whether or not these are novel species. Nevertheless, this suggests the possibility that they could be unstudied or rare bacteria. The Helmcken Falls cave microbiome possesses a great diversity of microbes with the potential for studies of novel microbial interactions and the isolation of new types of antimicrobial agents.


The mineralogical study of the Grotta Inferiore di Sant’Angelo (southern Italy), 2014, Catalano M. , Bloise A. , Miriello D. , Apollaro C. , Critelli T. , Muto F. , Cazzanelli E. , Barrese E.

In the present work, thirteen samples collected from the Grotta Inferiore di Sant’Angelo near the town of Cassano allo Jonio (Calabria region, southern Italy) were analyzed for their mineralogy. The Grotta Inferiore di Sant’Angelo is made up of subhorizontal, interlinked galleries between 400 and 450 meters above sea level. The floor is littered with deposits such as bat-guano, gypsum, and many speleothems that also cover the walls. The samples were identified and characterized by X-ray powder diffraction, scanning electron microscopy with energy dispersive spectrometer, microthermometry, and micro-Raman spectroscopy. The ten primary minerals identified in this study belong to six different groups: carbonate, sulfate, apatite, oxide and hydroxide, halide, and silicate. Clay minerals and eight other detrital minerals were also found: enstatite, rutile, magnesite, pyrite, chrysotile, quartz, dolomite, and chlorite. Characterization of cave minerals could be useful to improve the knowledge of the relation between them and the lithology of the host rocks


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