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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. ...

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. ...

Speleology in Kazakhstan

Shakalov on 11 Jul, 2012
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 endokarst is the part of a vertically layered karst system that is beneath the surface. endokarst includes the full spectrum of underground voids and the dissolutional features that are present on the rock surfaces surrounding them [9]. see also exokarst.?

Checkout all 2699 terms in the KarstBase Glossary of Karst and Cave Terms

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Featured articles from Cave & Karst Science Journals
Chemistry and Karst, White, William B.
Engineering challenges in Karst, Stevanović, Zoran; Milanović, Petar
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Featured articles from other Geoscience Journals
Geochemical and mineralogical fingerprints to distinguish the exploited ferruginous mineralisations of Grotta della Monaca (Calabria, Italy), Dimuccio, L.A.; Rodrigues, N.; Larocca, F.; Pratas, J.; Amado, A.M.; Batista de Carvalho, L.A.
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
See all featured articles from other geoscience journals

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Your search for biofilms (Keyword) returned 34 results for the whole karstbase:
Showing 16 to 30 of 34
Wurmfrmige Excentriques mit ungewhnlichem Calcitgefge - Untersuchungen mit der Elektronen-Rckstreu-Beugungs-Methode, 2007, Richter D. K. , Neuser R. D.
Vermiform helictites (excentriques) from a former side branch of the Breitscheid-Erdbach cave are frequently polycrystalline and not composed of a single calcite crystal. The electron backscatter diffraction (EBSD)-technique reveals a lath-shaped calcite structure with c-axes oriented nearly parallel to the elongation of the helictites. The resulting structure of the helictites is a calcite fibre bundle diverging along the growth direction. Three equivalent symmetrical sectors can be distinguished. The maximum deviation from the elongation is 18 and occurs at the exterior in the centre of the segments of the excentriques. The complex internal structure and the conical shape of the tip of the excentriques suggest a special kind of calcite precipitation, whereby biofilms seem to have played a significant role.

Niche differentiation among sulfur-oxidizing bacterial populations in cave waters, 2008, Jennifer L Macalady, Sharmishtha Dattagupta, Irene Schaperdoth, Daniel S Jones, Greg K Druschel And Danielle Eastman
The sulfidic Frasassi cave system affords a unique opportunity to investigate niche relationships among sulfur-oxidizing bacteria, including epsilonproteobacterial clades with no cultivated representatives. Oxygen and sulfide concentrations in the cave waters range over more than two orders of magnitude as a result of seasonally and spatially variable dilution of the sulfidic groundwater. A full-cycle rRNA approach was used to quantify dominant populations in biofilms collected in both diluted and undiluted zones. Sulfide concentration profiles within biofilms were obtained in situ using microelectrode voltammetry. Populations in rock-attached streamers depended on the sulfide/oxygen supply ratio of bulk water (r¼0.97; Po0.0001). Filamentous epsilonproteobacteria dominated at high sulfide to oxygen ratios (4150), whereas Thiothrix dominated at low ratios (o75). In contrast, Beggiatoa was the dominant group in biofilms at the sediment?water interface regardless of sulfide and oxygen concentrations or supply ratio. Our results highlight the versatility and ecological success of Beggiatoa in diffusion-controlled niches, and demonstrate that high sulfide/oxygen ratios in turbulent water are important for the growth of filamentous epsilonproteobacteria.

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

Cottonballs, a unique subaqeous moonmilk and abundant subaerial moonmilk in Cataract Cave, Tongass National Forest, Alaska, 2009, Curry M. D. , Boston P. J. , Spilde M. N. , Baichtal J. F. , Campbell A. R.
The Tongass National Forest is known for its world-class karst features and contains the largest concentration of dissolutional caves in Alaska. Within these karst systems exist unusual and possibly unique formations exhibiting possible biological origin or influence. Cataract Cave is an example of such a system. This cave hosts a unique depositional setting in which so-called cottonballs line two permanent pools. The cottonballs are a calcitic deposit heavily entwined within a mass of microbial filaments. They are juxtaposed with extensive subaerial calcitic moonmilk wall deposit of a more conventional nature but of an extraordinary thickness and abundance. Both the cottonballs and moonmilk are composed of microcrystalline aggregates (0.20 wt.%) compared to the cottonballs (0.12 wt.%). However, the cottonballs are dominated by monocrystalline needles, whereas the moonmilk is mainly composed of polycrystalline needles. The microbial environments of both displayed similar total microbial cell counts; however, culturable microbial counts varied between the deposits and among the various media. For both, in situ cultures and isolates inoculated in a calcium salt medium produced calcium carbonate mineralization within biofilms. Geochemical variations existed between the deposits. Moonmilk displayed a slightly higher abundance of organic carbon (0.20 wt%) compared to the cottonballs (0.12 wt%). Stable isotopic analysis revealed that the moonmilk (?13C = -1.6) was isotopically heavier compared to the cottonballs (?13C = -8.1) but both are lighter than the host rock (?13C = +1.1). However, the organic carbon ?13C values of both deposits were similar (?13C = -27.4 and 26.7) and isotopically lighter compared to other overlying surface organic carbon sources. Due to the similarities between the deposits, we infer that both the cottonballs and moonmilk are subject to a set of related processes that could collectively be accommodated by the term moonmilk. Thus, the cottonball pool formation can be characterized as a type of subaqueous moonmilk. The differences observed between the moonmilk and cottonballs may be largely attributable to the changes in the depositional environment, namely in air or water.

A recently evolved symbiosis between chemoautotrophic bacteria and a cave-dwelling amphipod, 2009, Dattagupta, S. , Schaperdoth, I. , Montanari, A. , Mariani, S. , Kita, N. , Valley, J. W. And Macalady, J. L.
Symbioses involving animals and chemoautotrophic bacteria form the foundation of entire ecosystems at deep-sea hydrothermal vents and cold seeps, but have so far not been reported in terrestrial or freshwater environments. A rare example of a terrestrial ecosystem sustained by chemoautotrophy is found within the sulfide-rich Frasassi limestone cave complex of central Italy. In this study, we report the discovery of abundant filamentous bacteria on the exoskeleton of Niphargus ictus, a macroinvertebrate endemic to Frasassi. Using 16S rDNA sequencing and fluorescence in situ hybridization (FISH), we show that N. ictus throughout the large cave complex are colonized by a single phylotype of bacteria in the sulfur-oxidizing clade Thiothrix. The epibiont phylotype is distinct from Thiothrix phylotypes that form conspicuous biofilms in the cave streams and pools inhabited by N. ictus. Using a combination of 13C labeling, FISH, and secondary ion mass spectrometry (SIMS), we show that the epibiotic Thiothrix are autotrophic, establishing the first known example of a non-marine chemoautotroph-animal symbiosis. Conditions supporting chemoautotrophy, and the N. ictus-Thiothrix association, likely commenced in the Frasassi cave complex between 350 000 and 1 million years ago. Therefore, the N. ictus-Thiothrix symbiosis is probably significantly younger than marine chemoautotrophic symbioses, many of which have been evolving for tens to hundreds of million years.

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.


Cottonballs, a unique subaqeous moonmilk and abundant subaerial moonmilk in Cataract Cave, Tongass National Forest, Alaska, 2009, Curry M. D. , Boston P. J. , Spilde. M. N. , Baichtal J. F. , Campbell A. R.

The Tongass National Forest is known for its world-class karst features and contains the largest concentration of dissolutional caves in Alaska. Within these karst systems exist unusual and possibly unique formations exhibiting possible biological origin or influence. Cataract Cave is an example of such a system. This cave hosts a unique depositional setting in which so-called “cottonballs� line two permanent pools. The cottonballs are a calcitic deposit heavily entwined within a mass of microbial filaments. They are juxtaposed with extensive subaerial calcitic moonmilk wall deposit of a more conventional nature but of an extraordinary thickness and abundance. Both the cottonballs and moonmilk are composed of microcrystalline aggregates (0.20 wt.%) compared to the cottonballs (0.12 wt.%). However, the cottonballs are dominated by monocrystalline needles, whereas the moonmilk is mainly composed of polycrystalline needles. The microbial environments of both displayed similar total microbial cell counts; however, culturable microbial counts varied between the deposits and among the various media. For both, in situ cultures and isolates inoculated in a calcium salt medium produced calcium carbonate mineralization within biofilms. Geochemical variations existed between the deposits. Moonmilk displayed a slightly higher abundance of organic carbon (0.20 wt%) compared to the cottonballs (0.12 wt%). Stable isotopic analysis revealed that the moonmilk (δ13C = -1.6‰) was isotopically heavier compared to the cottonballs (δ13C = -8.1‰) but both are lighter than the host rock (δ13C = +1.1‰). However, the organic carbon δ13C values of both deposits were similar (δ13C = -27.4 and –26.7‰) and isotopically lighter compared to other overlying surface organic carbon sources. Due to the similarities between the deposits, we infer that both the cottonballs and moonmilk are subject to a set of related processes that could collectively be accommodated by the term “moonmilk�. Thus, the cottonball pool formation can be characterized as a type of subaqueous moonmilk. The differences observed between the moonmilk and cottonballs may be largely attributable to the changes in the depositional environment, namely in air or water.


Genesis and functioning of the Aix-les-Bains hydrothermal karst (Savoie, France): past research and recent advances, 2010, Hoblea F. , Gallinojosnin S. , Audra Ph.

Aix-les-Bains (Savoie, France) owes its name and reputation to the thermal springs that occur along the eastern shore of Lake Bourget, France largest natural lake. Although the city waters have been exploited since Antiquity, scientific investigations into the nature and characteristics of the hydrothermal karst from which they emerge did not begin until the early 19th century. The present article traces the history of these investigations and summarizes the results of more than two centuries of scientific research. Today, the only visible signs of karstification related to hydrothermal flows are to be found in the discharge zone in the Urgonian limestone anticline that rises above the city centre. These features are: – the Grotte des Serpents, which houses the Alun Spring, the system main natural discharge, – the Chevalley Aven, a blind chimney that was accidentally uncovered in 1996, – other hydrothermal springs that are too small to enter, including the Soufre Spring. Although scientific investigation of the thermal springs at Aix-les-Bains began in the early 19th century, it was not until the 1920s that scientists started examining the relationship between karstification and the state of the aquifer. E.A.Martel was the first researcher to describe the Aix-les-Bains site as an active hydrothermal karst, in a pioneering study published in 1935. Sixty years later, the discovery of the Chevalley Aven during building work on a new hydrotherapy center gave fresh impetus to research into the karstification of the Aix-les-Bains thermo-mineral aquifer. Recent studies have also investigated the deep aquifer below the karst, using data provided by boreholes. The Urgonian limestone karst at Aix-les-Bains is the site of mixing between thermal waters rising through the anticline and meteoric waters percolating from the surface. Meteoric infiltration is sufficiently high for the hydrological behavior of the thermal springs to be identical to that of exsurgences in gravity-fed, cold-water transmissive karsts. The Chevalley Aven is a shaft that descends 30 meters below the surface, thereby providing access to the ground-water at depth. Monitoring of the water quality in the aven has shown that the Legionella contamination of the springs was due to high concentrations of the bacteria in upstream passages in the karst. In 2006, dye-tracing tests confirmed the existence of a hydraulic connection between the Chevalley Aven and the Alun and Soufre Springs, the fact there is a single ascending hydrothermal conduit, which lies between the Chevalley Aven and the Alun Spring. In addition to providing a valuable source of information about the functioning of the thermo-mineral aquifer, the cavities at Aix-les-Bains are of great karstological interest, especially for the study of hypogene speleogenetic processes. The circulation of warm (40oC), sulfur-rich waters and vapours through the system has led to the development of conduits with specific morphologies and the precipitation of characteristic deposits. These features include: – “beaded” chimneys and galleries formed by the linking of spheres produced by condensation-corrosion. Diffuse karstification along bedding planes around the main conduit; – deposition of non-carbonate minerals (gypsum, native sulfur); – formation of biothems and biofilms on walls subject to condensation. The Grotte des Serpents is a horizontal cavity that formed at the upper limit of the water table. The Chevalley Aven is a hypogene chimney that was sculpted under vadose conditions by the release of sulfuric acid-rich vapours above the thermal water table. As well as a surface coating of microbial mats and the presence of bacterial flakes in the thermal water, the vadose parts of the Aix-les-Bains hydrothermal karst contain a characteristic microfauna and flora. These microorganisms are thought to play an active role in hypogene karstification processes.


Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy, 2010, Jones D. S. , Tobler D. J. , Schaperdoth I. , Mainiero M. , Macalady J. L.

We performed a microbial community analysis of biofilms inhabiting thermal (35 to 50°C) waters more than 60m below the ground surface near Acquasanta Terme, Italy. The groundwater hosting the biofilms has 400 to 830 mkM sulfide, <10 mkM O2, pH of 6.3 to 6.7, and specific conductivity of 8,500 to 10,500 mkS/cm. Based on the results of 16S rRNA gene cloning and fluorescent in situ hybridization (FISH), the biofilms have low species richness, and lithoautotrophic (or possibly mixotrophic) Gamma- and Epsilonproteobacteria are the principle biofilm architects. Deltaproteobacteria sequences retrieved from the biofilms have <90% 16S rRNA similarity to their closest relatives in public databases and may represent novel sulfate-reducing bacteria. The Acquasanta biofilms share few species in common with Frasassi cave biofilms (13°C, 80 km distant) but have a similar community structure, with representatives in the same major clades. The ecological success of Sulfurovumales-group Epsilonproteobacteria in the Acquasanta biofilms is consistent with previous observations of their dominance in sulfidic cave waters with turbulent water flow and high dissolved sulfide/oxygen ratios.


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.


Distribution survey of Cyanobacteria in three Greek caves of Peloponnese, 2012, Lamprinou V. , Danielidis D. B. , Economouamilli A. , Pantazidou A.

Caves and hypogean environments host various phototrophic microorganisms, with Cyanobacteria constituting the major group. The spatial and temporal distribution of Cyanobacteria (156 taxa in total) from three Greek caves, located in the limestone arc of Peloponnese and differing in morphology, was studied. The community patterns in different ecological niches were analyzed in relation to environmental parameters (Photosynthetically Active Radiation, Temperature, and Relative Humidity). Cyanobacterial communities were found to thrive in patchy biofilms and showed known protective strategies against desiccation and irradiation. The nMDS analysis of the cumulative seasonal samples per sampling site showed no general pattern of distribution, with a clear differentiation of cyanobacterial communities among the three caves. Only in the typical cave ‘Kastria’, cyanobacterial taxa showed growth habits in accordance with the gradient of light from entrance inwards.


Biospeleogenesis, 2013, Barton, H. A.

Microorganisms have shaped the world around us, yet their role in karst processes and speleogenesis remains poorly understood. Biospeleogenesis is the formation of subsurface cavities and caves through the activities of microorganisms, by either respiratory (redox) or metabolic chemistries. In carrying out energy acquisition and the metabolic processes of growth, microorganisms change the local geochemistry of the environment. Such activities can dramatically accelerate speleogenesis and even lead to cave formation in geochemical environments that would otherwise not be conducive to dissolution. The aim of this chapter is to help the reader understand the importance of microbial activity in geochemistry and how such activity can lead to the formation and morphology of caves. The chapter then describes the role that microorganisms are known to have in speleogenesis (carbonic and sulfuric acid biospeleogenesis), hints that such activity may be occurring in newly described cave systems (iron biospeleogenesis), and a potential role in other cave systems (quartzite biospeleogenesis). It is hoped that the reader will gain an understanding of what motivates microorganisms to dramatically change their environment, understand the potential geochemical conditions where such activity could occur, and allow the informed geologist to make predictive statements as to the potential of, and for, biospeleogenesis 


Chemical characterization of biofilms formed in hypogene spring caves of Budapest, 2013, Savoly Zoltan, Dobosy Peter, Barkacs Katalin, Erő, Ss Anita, Kuzmann Ernő, , Homonnay Zoltan, Madlsző, Nyi Judit, Zaray Gyula

Chemical characterization of biofilms formed in hypogene spring caves of Budapest, 2013, Svoly Z. , Dobosy P. , Barkcs K. , Erő, Ss A. , Kuzmann E.

Insights into Cave Architecture and the Role of Bacterial Biofilm, 2013,

Caves offer a stable and protected environment from harsh and changing outside conditions. They lend living proof of the presence of minute life forms that delve deep within the earth’s crust where the possibility of life seems impossible. Devoid of all light sources and lacking the most common source of energy supplied through photosynthesis, the mysterious microbial kingdom in caves are consequently dependent upon alternative sources of energy derived from the surrounding atmosphere, minerals and rocks. There are a number of features that can be observed within a cave that may serve as evidence of microbial activity, for example, formation of biofilms comprised of multiple layers of microbial communities held together by protective gel-like polymers which form complex structures. Different bacterial biofilms can develop on the walls of the cave which can be visually distinguished by their colorations. Moreover, the pH generated by the metabolism of bacterial biofilm on the cave environment can lead to precipitation or dissolution of minerals in caves. Caves also offer an excellent scenario for studying biomineralization processes. The findings on the association of bacteria with secondary minerals as mentioned in this review will help to expand the existing knowledge in geomicrobiology and specifically on the influence of microorganisms in the formation of cave deposits. This paper reviews the current state of knowledge of biospeleology of caves and the associated bacterial biofilms. Recommendations for future research are mentioned to encourage a drift from qualitative studies to more experimental studies.


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